diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..4039b59 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,33 @@ +root = true + +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +trim_trailing_whitespace = true +indent_size = 4 +indent_style = space + +[*.{md,yml,yaml,html,css,scss,js,cff}] +indent_size = 2 + +# These files are edited and tested upstream in nf-core/modules +[/modules/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset +indent_size = unset + +# Unset for allele references +[/data/references/alleles*] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset +indent_size = unset + +[/assets/email*] +indent_size = unset diff --git a/.gitattributes b/.gitattributes index 7fe5500..050bb12 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ *.config linguist-language=nextflow +modules/nf-core/** linguist-generated +subworkflows/nf-core/** linguist-generated diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml index 030138a..191fabd 100644 --- a/.github/.dockstore.yml +++ b/.github/.dockstore.yml @@ -3,3 +3,4 @@ version: 1.2 workflows: - subclass: nfl primaryDescriptorPath: /nextflow.config + publish: True diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 0577938..b4bb3f8 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -15,11 +15,11 @@ Contributions to the code are even more welcome ;) If you'd like to write some code for nf-core/hlatyping, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/hlatyping issues](https://github.com/nf-core/hlatyping/issues) to avoid duplicating work - * If there isn't one already, please create one so that others know you're working on this +1. Check that there isn't already an issue about your idea in the [nf-core/hlatyping issues](https://github.com/nf-core/hlatyping/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/hlatyping repository](https://github.com/nf-core/hlatyping) to your GitHub account -3. Make the necessary changes / additions within your forked repository -4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged +3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) +4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -30,14 +30,14 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t There are typically two types of tests that run: -### Lint Tests +### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. -### Pipeline Tests +### Pipeline tests Each `nf-core` pipeline should be set up with a minimal set of test-data. `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. @@ -48,10 +48,56 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -* On your own fork, make a new branch `patch` based on `upstream/master`. -* Fix the bug, and bump version (X.Y.Z+1). -* A PR should be made on `master` from patch to directly this particular bug. +- On your own fork, make a new branch `patch` based on `upstream/master`. +- Fix the bug, and bump version (X.Y.Z+1). +- A PR should be made on `master` from patch to directly this particular bug. ## Getting help -For further information/help, please consult the [nf-core/hlatyping documentation](https://nf-co.re/hlatyping/docs) and don't hesitate to get in touch on the nf-core Slack [#hlatyping](https://nfcore.slack.com/channels/hlatyping) channel ([join our Slack here](https://nf-co.re/join/slack)). +For further information/help, please consult the [nf-core/hlatyping documentation](https://nf-co.re/hlatyping/usage) and don't hesitate to get in touch on the nf-core Slack [#hlatyping](https://nfcore.slack.com/channels/hlatyping) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## Pipeline contribution conventions + +To make the nf-core/hlatyping code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. + +### Adding a new step + +If you wish to contribute a new step, please use the following coding standards: + +1. Define the corresponding input channel into your new process from the expected previous process channel +2. Write the process block (see below). +3. Define the output channel if needed (see below). +4. Add any new parameters to `nextflow.config` with a default (see below). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +6. Add sanity checks and validation for all relevant parameters. +7. Perform local tests to validate that the new code works as expected. +8. If applicable, add a new test command in `.github/workflow/ci.yml`. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. + +### Default values + +Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. + +Once there, use `nf-core schema build` to add to `nextflow_schema.json`. + +### Default processes resource requirements + +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. + +The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. + +### Naming schemes + +Please use the following naming schemes, to make it easy to understand what is going where. + +- initial process channel: `ch_output_from_` +- intermediate and terminal channels: `ch__for_` + +### Nextflow version bumping + +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` + +### Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 5a659f2..0000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,45 +0,0 @@ - - -## Description of the bug - - - -## Steps to reproduce - -Steps to reproduce the behaviour: - -1. Command line: -2. See error: - -## Expected behaviour - - - -## System - -- Hardware: -- Executor: -- OS: -- Version - -## Nextflow Installation - -- Version: - -## Container engine - -- Engine: -- version: -- Image tag: - -## Additional context - - diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml new file mode 100644 index 0000000..97325f1 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -0,0 +1,50 @@ +name: Bug report +description: Report something that is broken or incorrect +labels: bug +body: + - type: markdown + attributes: + value: | + Before you post this issue, please check the documentation: + + - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) + - [nf-core/hlatyping pipeline documentation](https://nf-co.re/hlatyping/usage) + + - type: textarea + id: description + attributes: + label: Description of the bug + description: A clear and concise description of what the bug is. + validations: + required: true + + - type: textarea + id: command_used + attributes: + label: Command used and terminal output + description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. + render: console + placeholder: | + $ nextflow run ... + + Some output where something broke + + - type: textarea + id: files + attributes: + label: Relevant files + description: | + Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. + Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. + + - type: textarea + id: system + attributes: + label: System information + description: | + * Nextflow version _(eg. 21.10.3)_ + * Hardware _(eg. HPC, Desktop, Cloud)_ + * Executor _(eg. slurm, local, awsbatch)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * OS _(eg. CentOS Linux, macOS, Linux Mint)_ + * Version of nf-core/hlatyping _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000..cdc71b2 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,7 @@ +contact_links: + - name: Join nf-core + url: https://nf-co.re/join + about: Please join the nf-core community here + - name: "Slack #hlatyping channel" + url: https://nfcore.slack.com/channels/hlatyping + about: Discussion about the nf-core/hlatyping pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index 2e67964..0000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,26 +0,0 @@ - - -## Is your feature request related to a problem? Please describe - - - - - -## Describe the solution you'd like - - - -## Describe alternatives you've considered - - - -## Additional context - - diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 0000000..41f9f36 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature request +description: Suggest an idea for the nf-core/hlatyping pipeline +labels: enhancement +body: + - type: textarea + id: description + attributes: + label: Description of feature + description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. + validations: + required: true diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 0fc09a7..bb6449a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -13,8 +13,12 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hlat ## PR checklist -- [ ] This comment contains a description of changes (with reason) -- [ ] `CHANGELOG.md` is updated +- [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] Documentation in `docs` is updated -- [ ] If necessary, also make a PR on the [nf-core/hlatyping branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/hlatyping) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hlatyping/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/hlatyping _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Usage Documentation in `docs/usage.md` is updated. +- [ ] Output Documentation in `docs/output.md` is updated. +- [ ] `CHANGELOG.md` is updated. +- [ ] `README.md` is updated (including new tool citations and authors/contributors). diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml index 96b12a7..7fad5f1 100644 --- a/.github/markdownlint.yml +++ b/.github/markdownlint.yml @@ -2,4 +2,4 @@ default: true, line-length: false no-duplicate-header: - siblings_only: true + siblings_only: true diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8ed0ca1..80203ec 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,36 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on push to the master branch. +# This workflow is triggered on published releases. +# It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: release: types: [published] - + workflow_dispatch: jobs: - run-awstest: + run-tower: name: Run AWS full tests if: github.repository == 'nf-core/hlatyping' runs-on: ubuntu-latest steps: - - name: Setup Miniconda - uses: goanpeca/setup-miniconda@v1.0.2 + - name: Launch workflow via tower + uses: nf-core/tower-action@v3 + # Add full size test data (but still relatively small datasets for few samples) + # on the `test_full.config` test runs with only one set of parameters + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hlatyping/work-${{ github.sha }} + parameters: | + { + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hlatyping/results-${{ github.sha }}" + } + profiles: test_full,aws_tower + - uses: actions/upload-artifact@v3 with: - auto-update-conda: true - python-version: 3.7 - - name: Install awscli - run: conda install -c conda-forge awscli - - name: Start AWS batch job - env: - AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} - AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} - AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} - AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} - AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} - run: | - aws batch submit-job \ - --region eu-west-1 \ - --job-name nf-core-hlatyping \ - --job-queue $AWS_JOB_QUEUE \ - --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/hlatyping", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/hlatyping/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hlatyping/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + name: Tower debug log file + path: tower_action_*.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 77df7b0..a8ab21b 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -1,37 +1,29 @@ name: nf-core AWS test -# This workflow is triggered on push to the master branch. +# This workflow can be triggered manually with the GitHub actions workflow dispatch button. # It runs the -profile 'test' on AWS batch on: - push: - branches: - - master - + workflow_dispatch: jobs: - run-awstest: + run-tower: name: Run AWS tests if: github.repository == 'nf-core/hlatyping' runs-on: ubuntu-latest steps: - - name: Setup Miniconda - uses: goanpeca/setup-miniconda@v1.0.2 + # Launch workflow using Tower CLI tool action + - name: Launch workflow via tower + uses: nf-core/tower-action@v3 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hlatyping/work-${{ github.sha }} + parameters: | + { + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hlatyping/results-test-${{ github.sha }}" + } + profiles: test,aws_tower + - uses: actions/upload-artifact@v3 with: - auto-update-conda: true - python-version: 3.7 - - name: Install awscli - run: conda install -c conda-forge awscli - - name: Start AWS batch job - env: - AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} - AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} - AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} - AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} - AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} - run: | - aws batch submit-job \ - --region eu-west-1 \ - --job-name nf-core-hlatyping \ - --job-queue $AWS_JOB_QUEUE \ - --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/hlatyping", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hlatyping/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hlatyping/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + name: Tower debug log file + path: tower_action_*.log diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 18f21b1..c1014d9 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -2,7 +2,7 @@ name: nf-core branch protection # This workflow is triggered on PRs to master branch on the repository # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` on: - pull_request: + pull_request_target: branches: [master] jobs: @@ -13,8 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/hlatyping' run: | - { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/hlatyping ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hlatyping ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -23,15 +22,23 @@ jobs: uses: mshick/add-pr-comment@v1 with: message: | + ## This PR is against the `master` branch :x: + + * Do not close this PR + * Click _Edit_ and change the `base` to `dev` + * This CI test will remain failed until you push a new commit + + --- + Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch. + Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. + Note that even after this, the test will continue to show as failing until you push a new commit. Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} allow-repeats: false - diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ed544a7..f68a360 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,85 +8,53 @@ on: release: types: [published] +env: + NXF_ANSI_LOG: false + jobs: test: - name: Run workflow tests + name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hlatyping') }} + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hlatyping') }}" runs-on: ubuntu-latest - env: - NXF_VER: ${{ matrix.nxf_ver }} - NXF_ANSI_LOG: false strategy: matrix: - # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['19.10.0', ''] + NXF_VER: + - "21.10.3" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v2 - - name: Check if Dockerfile or Conda environment changed - uses: technote-space/get-diff-action@v1 - with: - PREFIX_FILTER: | - Dockerfile - environment.yml - - - name: Build new docker image - if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/hlatyping:1.2.0 - - - name: Pull docker image - if: ${{ !env.GIT_DIFF }} - run: | - docker pull nfcore/hlatyping:dev - docker tag nfcore/hlatyping:dev nfcore/hlatyping:1.2.0 - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Run pipeline with test data + # For example: adding multiple test runs with different parameters + # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker - + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results profile: name: Run profile tests if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hlatyping') }} runs-on: ubuntu-latest - env: - NXF_VER: '19.10.0' - NXF_ANSI_LOG: false strategy: matrix: - tests: ['test_fastq', 'test_rna'] + NXF_VER: + - "21.10.3" + - "latest-everything" + tests: ["test_fastq", "test_rna", "test_dna_rna"] steps: - name: Check out pipeline code uses: actions/checkout@v2 - - - name: Check if Dockerfile or Conda environment changed - uses: technote-space/get-diff-action@v1 - with: - PREFIX_FILTER: | - Dockerfile - environment.yml - - - name: Build new docker image - if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/hlatyping:1.2.0 - - - name: Pull docker image - if: ${{ !env.GIT_DIFF }} - run: | - docker pull nfcore/hlatyping:dev - docker tag nfcore/hlatyping:dev nfcore/hlatyping:1.2.0 - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Run pipeline with profile ${{ matrix.tests }} run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker \ No newline at end of file + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml new file mode 100644 index 0000000..4525cde --- /dev/null +++ b/.github/workflows/fix-linting.yml @@ -0,0 +1,55 @@ +name: Fix linting from a comment +on: + issue_comment: + types: [created] + +jobs: + deploy: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot fix linting') && + github.repository == 'nf-core/hlatyping' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@v3 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + - uses: actions/setup-node@v2 + + - name: Install Prettier + run: npm install -g prettier @prettier/plugin-php + + # Check that we actually need to fix something + - name: Run 'prettier --check' + id: prettier_status + run: | + if prettier --check ${GITHUB_WORKSPACE}; then + echo "::set-output name=result::pass" + else + echo "::set-output name=result::fail" + fi + + - name: Run 'prettier --write' + if: steps.prettier_status.outputs.result == 'fail' + run: prettier --write ${GITHUB_WORKSPACE} + + - name: Commit & push changes + if: steps.prettier_status.outputs.result == 'fail' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Fix linting with Prettier" + git push diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8e8d5bb..8a5ce69 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,7 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines +# It runs the `nf-core lint` and markdown lint tests to ensure +# that the code meets the nf-core guidelines. on: push: pull_request: @@ -8,44 +9,75 @@ on: types: [published] jobs: - Markdown: + EditorConfig: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' - - name: Install markdownlint - run: npm install -g markdownlint-cli - - name: Run Markdownlint - run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml - YAML: + + - uses: actions/setup-node@v2 + + - name: Install editorconfig-checker + run: npm install -g editorconfig-checker + + - name: Run ECLint check + run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') + + Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 + - uses: actions/checkout@v2 + + - uses: actions/setup-node@v2 + + - name: Install Prettier + run: npm install -g prettier + + - name: Run Prettier --check + run: prettier --check ${GITHUB_WORKSPACE} + + PythonBlack: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + - name: Check code lints with Black + uses: psf/black@stable + + # If the above check failed, post a comment on the PR explaining the failure + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 with: - node-version: '10' - - name: Install yaml-lint - run: npm install -g yaml-lint - - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml") + message: | + ## Python linting (`black`) is failing + + To keep the code consistent with lots of contributors, we run automated code consistency checks. + To fix this CI test, please run: + + * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` + * Fix formatting errors in your pipeline: `black .` + + Once you push these changes the test should pass, and you can hide this comment :+1: + + We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + nf-core: runs-on: ubuntu-latest steps: - - name: Check out pipeline code uses: actions/checkout@v2 - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v1 + - uses: actions/setup-python@v3 with: - python-version: '3.6' - architecture: 'x64' + python-version: "3.7" + architecture: "x64" - name: Install dependencies run: | @@ -57,12 +89,18 @@ jobs: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} + run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Save PR number + if: ${{ always() }} + run: echo ${{ github.event.pull_request.number }} > PR_number.txt - name: Upload linting log file artifact if: ${{ always() }} uses: actions/upload-artifact@v2 with: - name: linting-log-file - path: lint_log.txt - + name: linting-logs + path: | + lint_log.txt + lint_results.md + PR_number.txt diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml new file mode 100644 index 0000000..04758f6 --- /dev/null +++ b/.github/workflows/linting_comment.yml @@ -0,0 +1,28 @@ +name: nf-core linting comment +# This workflow is triggered after the linting action is complete +# It posts an automated comment to the PR, even if the PR is coming from a fork + +on: + workflow_run: + workflows: ["nf-core linting"] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: Download lint results + uses: dawidd6/action-download-artifact@v2 + with: + workflow: linting.yml + workflow_conclusion: completed + + - name: Get PR number + id: pr_number + run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)" + + - name: Post PR comment + uses: marocchino/sticky-pull-request-comment@v2 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.pr_number.outputs.pr_number }} + path: linting-logs/lint_results.md diff --git a/.github/workflows/push_dockerhub.yml b/.github/workflows/push_dockerhub.yml deleted file mode 100644 index 720f3f5..0000000 --- a/.github/workflows/push_dockerhub.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: nf-core Docker push -# This builds the docker image and pushes it to DockerHub -# Runs on nf-core repo releases and push event to 'dev' branch (PR merges) -on: - push: - branches: - - dev - release: - types: [published] - -jobs: - push_dockerhub: - name: Push new Docker image to Docker Hub - runs-on: ubuntu-latest - # Only run for the nf-core repo, for releases and merged PRs - if: ${{ github.repository == 'nf-core/hlatyping' }} - env: - DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }} - DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }} - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Build new docker image - run: docker build --no-cache . -t nfcore/hlatyping:latest - - - name: Push Docker image to DockerHub (dev) - if: ${{ github.event_name == 'push' }} - run: | - echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin - docker tag nfcore/hlatyping:latest nfcore/hlatyping:dev - docker push nfcore/hlatyping:dev - - - name: Push Docker image to DockerHub (release) - if: ${{ github.event_name == 'release' }} - run: | - echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin - docker push nfcore/hlatyping:latest - docker tag nfcore/hlatyping:latest nfcore/hlatyping:${{ github.event.release.tag_name }} - docker push nfcore/hlatyping:${{ github.event.release.tag_name }} diff --git a/.gitignore b/.gitignore index 14fa282..5124c9a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,8 @@ .nextflow* work/ +data/ results/ .DS_Store -tests/ testing/ testing* *.pyc - diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 0000000..85d95ec --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,14 @@ +image: nfcore/gitpod:latest + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.nf-core.yml b/.nf-core.yml new file mode 100644 index 0000000..3805dc8 --- /dev/null +++ b/.nf-core.yml @@ -0,0 +1 @@ +repository_type: pipeline diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..eb74a57 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,10 @@ +email_template.html +adaptivecard.json +.nextflow* +work/ +data/ +results/ +.DS_Store +testing/ +testing* +*.pyc diff --git a/.prettierrc.yml b/.prettierrc.yml new file mode 100644 index 0000000..c81f9a7 --- /dev/null +++ b/.prettierrc.yml @@ -0,0 +1 @@ +printWidth: 120 diff --git a/CHANGELOG.md b/CHANGELOG.md index 7278a19..4071fad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,25 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 2.0.0 - Han Solo - 2022-10-18 + +### `Added` + +- [#141](https://github.com/nf-core/hlatyping/pull/141) - Add `OptiType` results to `MultiQC` report + +### `Changed` + +- [#140](https://github.com/nf-core/hlatyping/pull/140) - Port pipeline to `DSL2` +- [#140](https://github.com/nf-core/hlatyping/pull/140) - Merge nf-core template updates up to `2.6` +- [#140](https://github.com/nf-core/hlatyping/pull/140) - Support for BAM and FASTQ input in the same run +- [#140](https://github.com/nf-core/hlatyping/pull/140) - Support for DNA and RNA input in the same run + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## 1.2.0 - lead-sparrow - 2020-08-21 ### `Added` @@ -54,4 +73,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## 1.0.0 - 2018-07-17 -Initial release of nf-core/hlatyping, created with the [NGI-NF cookiecutter template](https://github.com/ewels/NGI-NFcookiecutter). +# Initial release of nf-core/hlatyping, created with the [NGI-NF cookiecutter template](https://github.com/ewels/NGI-NFcookiecutter) diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..017666c --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,56 @@ +cff-version: 1.2.0 +message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" +authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Garcia + given-names: Maxime Ulysse + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven +title: "The nf-core framework for community-curated bioinformatics pipelines." +version: 2.4.1 +doi: 10.1038/s41587-020-0439-x +date-released: 2022-05-16 +url: https://github.com/nf-core/tools +prefered-citation: + type: article + authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Garcia + given-names: Maxime Ulysse + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven + doi: 10.1038/s41587-020-0439-x + journal: nature biotechnology + start: 276 + end: 278 + title: "The nf-core framework for community-curated bioinformatics pipelines." + issue: 3 + volume: 38 + year: 2020 + url: https://dx.doi.org/10.1038/s41587-020-0439-x diff --git a/CITATIONS.md b/CITATIONS.md new file mode 100644 index 0000000..9f23ca6 --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1,49 @@ +# nf-core/hlatyping: Citations + +## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) + +> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. + +## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) + +> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. + +## Pipeline tools + +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + +- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) + + > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943; PMCID: PMC2723002. + +- [Yara](https://www.seqan.de/apps/yara.html) + + > Siragusa E, Weese D, Reinert K. Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res. 2013 Apr;41(7):e78. doi: 10.1093/nar/gkt005. Epub 2013 Jan 28. PMID: 23358824; PMCID: PMC3627565. + + > Siragusa, E. Approximate string matching for high-throughput sequencing. Diss. 2015. + +- [OptiType](https://pubmed.ncbi.nlm.nih.gov/25143287/) + + > Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics. 2014 Dec 1;30(23):3310-6. doi: 10.1093/bioinformatics/btu548. Epub 2014 Aug 20. PMID: 25143287; PMCID: PMC4441069. + +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + +## Software packaging/containerisation tools + +- [Anaconda](https://anaconda.com) + + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. + +- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) + + > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. + +- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) + + > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. + +- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + +- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 405fb1b..f4fd052 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,46 +1,111 @@ -# Contributor Covenant Code of Conduct +# Code of Conduct at nf-core (v1.0) ## Our Pledge -In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: -## Our Standards +- Age +- Body size +- Familial status +- Gender identity and expression +- Geographical location +- Level of experience +- Nationality and national origins +- Native language +- Physical and neurological ability +- Race or ethnicity +- Religion +- Sexual identity and orientation +- Socioeconomic status -Examples of behavior that contributes to creating a positive environment include: +Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance. -* Using welcoming and inclusive language -* Being respectful of differing viewpoints and experiences -* Gracefully accepting constructive criticism -* Focusing on what is best for the community -* Showing empathy towards other community members +## Preamble -Examples of unacceptable behavior by participants include: +> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. -* The use of sexualized language or imagery and unwelcome sexual attention or advances -* Trolling, insulting/derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or electronic address, without explicit permission -* Other conduct which could reasonably be considered inappropriate in a professional setting +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. + +nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. + +We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. + +Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. + +We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. + +Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re ## Our Responsibilities -Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. +The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. + +The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. 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This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. + +All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. + +## Procedures for Reporting CoC violations -Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -## Scope +You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). -This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. +Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. -## Enforcement +All reports will be handled with utmost discretion and confidentially. -Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. +## Attribution and Acknowledgements -Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. +- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4) +- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition) +- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/) +- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla) -## Attribution +## Changelog -This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version] +### v1.0 - March 12th, 2021 -[homepage]: https://contributor-covenant.org -[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/ +- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 16af97c..0000000 --- a/Dockerfile +++ /dev/null @@ -1,17 +0,0 @@ -FROM nfcore/base:1.10.2 -LABEL authors="Christopher Mohr, Alexander Peltzer, Sven Fillinger" \ - description="Docker image containing all software requirements for the nf-core/hlatyping pipeline" - -# Install the conda environment -COPY environment.yml / -RUN conda env create --quiet -f /environment.yml && conda clean -a - -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-hlatyping-1.2.0/bin:$PATH - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-hlatyping-1.2.0 > nf-core-hlatyping-1.2.0.yml - -# Instruct R processes to use these empty files instead of clashing with a local version -RUN touch .Rprofile -RUN touch .Renviron \ No newline at end of file diff --git a/README.md b/README.md index bd047f6..e523373 100644 --- a/README.md +++ b/README.md @@ -1,65 +1,64 @@ -# ![nf-core/hlatyping](docs/images/nf-core-hlatyping_logo.png) +# ![nf-core/hlatyping](docs/images/nf-core-hlatyping_logo_light.png#gh-light-mode-only) ![nf-core/hlatyping](docs/images/nf-core-hlatyping_logo_dark.png#gh-dark-mode-only) -[![GitHub Actions CI Status](https://github.com/nf-core/hlatyping/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/hlatyping/actions) -[![GitHub Actions Linting Status](https://github.com/nf-core/hlatyping/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/hlatyping/actions) -[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1401039.svg)](https://doi.org/10.5281/zenodo.1401039) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/hlatyping/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1401039-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1401039) -[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/) -[![Docker](https://img.shields.io/docker/automated/nfcore/hlatyping.svg)](https://hub.docker.com/r/nfcore/hlatyping) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hlatyping-4A154B?logo=slack)](https://nfcore.slack.com/channels/hlatyping) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) +[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/hlatyping) + +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hlatyping-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hlatyping)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction +**nf-core/hlatyping** is a bioinformatics best-practice analysis pipeline for Precision HLA typing from next-generation sequencing data. The pipeline does next-generation sequencing-based Human Leukozyte Antigen (HLA) typing using [OptiType](https://github.com/FRED-2/OptiType). OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are considered simultaneously to find an allele combination that maximizes the number of explained reads. -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. - -## Quick Start - -1. Install [`nextflow`](https://nf-co.re/usage/installation) +The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! -2. Install either [`Docker`](https://docs.docker.com/engine/installation/) or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hlatyping/results). -3. Download the pipeline and test it on a minimal dataset with a single command: - - ```bash - nextflow run nf-core/hlatyping -profile test, - ``` +## Pipeline summary - > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - -4. Start running your own analysis! +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +2. Generate reference indices ([`yara`](https://www.seqan.de/apps/yara.html)) +3. Map reads to reference ([`yara`](https://www.seqan.de/apps/yara.html)) +4. Run HLA typing ([`OptiType`](https://github.com/FRED-2/OptiType)) +5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) - ```bash - nextflow run nf-core/hlatyping -profile --input '*_R{1,2}.fastq.gz' - ``` - -See [usage docs](https://nf-co.re/hlatyping/usage) for all of the available options when running the pipeline. +## Quick Start -## Documentation +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) -The nf-core/hlatyping pipeline comes with documentation about the pipeline which you can read at [https://nf-co.re/hlatyping](https://nf-co.re/hlatyping). +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. -### Pipeline DAG +3. Download the pipeline and test it on a minimal dataset with a single command: -The hlatyping pipeline can currently deal with two input formats: `.fastq{.gz}` or `.bam`, not both at the same time however. If the input file type is `bam`, than the pipeline extracts all reads from it and performs an mapping additional step with the `yara` mapper against the HLA reference sequence. Indices are provided in the `./data` directory of this repository. Optitype uses [razers3](https://github.com/seqan/seqan/tree/master/apps/razers3), which is very memory consuming. In order to avoid memory issues during pipeline execution, we reduce the mapping information on the relevant HLA regions on chromosome 6. + ```bash + nextflow run nf-core/hlatyping -profile test,YOURPROFILE --outdir + ``` -#### DAG with `.fastq{.gz}` as input + Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. -Creates a config file from the command line arguments, which is then passed to OptiType. In parallel, the fastqs are unzipped if they are passed as archives. OptiType is then used for the HLA typing. + > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. + > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. -![DAG with `fastq.{gz}` files](docs/images/hlatyping_dag_fastq.png) +4. Start running your own analysis! -#### DAG with `.bam` as input + ```bash + nextflow run nf-core/hlatyping --input samplesheet.csv --outdir -profile + ``` -Creates a config file from the command line arguments, which is then passed to OptiType. In parallel, the reads are extracted from the bam file and mapped again against the HLA reference sequence on chromosome 6. OptiType is then used for the HLA typing. +## Documentation -![DAG with `.bam` file](docs/images/hlatyping_dag_bam.png) +The nf-core/hlatyping pipeline comes with documentation about the pipeline [usage](https://nf-co.re/hlatyping/usage), [parameters](https://nf-co.re/hlatyping/parameters) and [output](https://nf-co.re/hlatyping/output). ## Credits -nf-core/hlatyping was originally written by [Christopher Mohr](https://github.com/christopher-mohr) from [Institute for Translational Bioinformatics](https://kohlbacherlab.org/team_tbi/) and [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/), [Alexander Peltzer](https://github.com/apeltzer) from [Boeheringer Ingelheim](https://www.boehringer-ingelheim.de), and [Sven Fillinger](https://github.com/sven1103) from [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/). +nf-core/hlatyping was originally written by [Christopher Mohr](https://github.com/christopher-mohr) from [Medical Data Integration Center](https://www.medizin.uni-tuebingen.de/de/das-klinikum/einrichtungen/institute/informationstechnologie-und-medizininformatik/medic) and [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/), [Alexander Peltzer](https://github.com/apeltzer) from [Boehringer Ingelheim](https://www.boehringer-ingelheim.de), and [Sven Fillinger](https://github.com/sven1103) from [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/). ## Contributions and Support @@ -67,9 +66,11 @@ If you would like to contribute to this pipeline, please see the [contributing g For further information or help, don't hesitate to get in touch on the [Slack `#hlatyping` channel](https://nfcore.slack.com/channels/hlatyping) (you can join with [this invite](https://nf-co.re/join/slack)). -## Citation +## Citations + +If you use nf-core/hlatyping for your analysis, please cite it using the following doi: [10.5281/zenodo.1401039](https://doi.org/10.5281/zenodo.1401039) -If you use nf-core/hlatyping for your analysis, please cite it using the following doi: [10.5281/zenodo.1401039](https://doi.org/10.5281/zenodo.1401039) +An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: @@ -78,4 +79,3 @@ You can cite the `nf-core` publication as follows: > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). -> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ) diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json new file mode 100644 index 0000000..6c07c50 --- /dev/null +++ b/assets/adaptivecard.json @@ -0,0 +1,67 @@ +{ + "type": "message", + "attachments": [ + { + "contentType": "application/vnd.microsoft.card.adaptive", + "contentUrl": null, + "content": { + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "msteams": { + "width": "Full" + }, + "type": "AdaptiveCard", + "version": "1.2", + "body": [ + { + "type": "TextBlock", + "size": "Large", + "weight": "Bolder", + "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", + "text": "nf-core/hlatyping v${version} - ${runName}", + "wrap": true + }, + { + "type": "TextBlock", + "spacing": "None", + "text": "Completed at ${dateComplete} (duration: ${duration})", + "isSubtle": true, + "wrap": true + }, + { + "type": "TextBlock", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", + "wrap": true + }, + { + "type": "TextBlock", + "text": "The command used to launch the workflow was as follows:", + "wrap": true + }, + { + "type": "TextBlock", + "text": "${commandLine}", + "isSubtle": true, + "wrap": true + } + ], + "actions": [ + { + "type": "Action.ShowCard", + "title": "Pipeline Configuration", + "card": { + "type": "AdaptiveCard", + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "body": [ + { + "type": "FactSet", + "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> + ] + } + ] + } + } + ] + } + } + ] +} diff --git a/assets/email_template.html b/assets/email_template.html index bb3eeee..2bdb79d 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,6 +1,5 @@ - diff --git a/assets/email_template.txt b/assets/email_template.txt index 5dcd8c2..aa4e83e 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -6,7 +6,6 @@ `._,._,' nf-core/hlatyping v${version} ---------------------------------------------------- - Run Name: $runName <% if (success){ diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml new file mode 100644 index 0000000..4620b96 --- /dev/null +++ b/assets/methods_description_template.yml @@ -0,0 +1,24 @@ +id: "nf-core-hlatyping-methods-description" +description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." +section_name: "nf-core/hlatyping Methods Description" +section_href: "https://github.com/nf-core/hlatyping" +plot_type: "html" +## You inject any metadata in the Nextflow '${workflow}' object +data: | +

Methods

+

Data was processed using nf-core/hlatyping v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

+ 
${workflow.commandLine}
+

References

+
    +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • +
+
+
Notes:
+
    + ${nodoi_text} +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • +
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • +
+
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml deleted file mode 100644 index 02576e9..0000000 --- a/assets/multiqc_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/hlatyping - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - software_versions: - order: -1000 - nf-core-hlatyping-summary: - order: -1001 - -export_plots: true diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml new file mode 100644 index 0000000..c47fcff --- /dev/null +++ b/assets/multiqc_config.yml @@ -0,0 +1,13 @@ +report_comment: > + This report has been generated by the nf-core/hlatyping + analysis pipeline. For information about how to interpret these results, please see the + documentation. +report_section_order: + "nf-core-hlatyping-methods-description": + order: -1000 + software_versions: + order: -1001 + "nf-core-hlatyping-summary": + order: -1002 + +export_plots: true diff --git a/assets/multiqc_optitype_config.yml b/assets/multiqc_optitype_config.yml new file mode 100644 index 0000000..da4e920 --- /dev/null +++ b/assets/multiqc_optitype_config.yml @@ -0,0 +1,2 @@ +table_columns_visible: + OptiType: True diff --git a/assets/nf-core-hlatyping_logo_light.png b/assets/nf-core-hlatyping_logo_light.png new file mode 100644 index 0000000..f8af40e Binary files /dev/null and b/assets/nf-core-hlatyping_logo_light.png differ diff --git a/assets/nf-core-hlatyping_social_preview.png b/assets/nf-core-hlatyping_social_preview.png deleted file mode 100644 index 3997219..0000000 Binary files a/assets/nf-core-hlatyping_social_preview.png and /dev/null differ diff --git a/assets/nf-core-hlatyping_social_preview.svg b/assets/nf-core-hlatyping_social_preview.svg deleted file mode 100644 index 6cafaa1..0000000 --- a/assets/nf-core-hlatyping_social_preview.svg +++ /dev/null @@ -1,448 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - Precision HLA typing from next-generation sequencing data - hlatyping - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv new file mode 100644 index 0000000..1edea3b --- /dev/null +++ b/assets/samplesheet.csv @@ -0,0 +1,3 @@ +sample,fastq_1,fastq_2,seq_type +SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,dna +SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,dna diff --git a/assets/schema_input.json b/assets/schema_input.json new file mode 100644 index 0000000..84f037b --- /dev/null +++ b/assets/schema_input.json @@ -0,0 +1,45 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/hlatyping/master/assets/schema_input.json", + "title": "nf-core/hlatyping pipeline - params.input schema", + "description": "Schema for the file provided with params.input", + "type": "array", + "items": { + "type": "object", + "properties": { + "sample": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Sample name must be provided and cannot contain spaces" + }, + "fastq_1": { + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + }, + "fastq_2": { + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$" + }, + { + "type": "string", + "maxLength": 0 + } + ] + }, + "seq_type": { + "errorMessage": "Sequencing type must be one of the following: 'dna', 'rna'", + "anyOf": [ + { + "type": "string", + "pattern": "^(dna|rna)$" + } + ] + } + }, + "required": ["sample", "fastq_1", "seq_type"] + } +} diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index cc532ba..0436558 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -12,18 +12,18 @@ $email_html Content-Type: image/png;name="nf-core-hlatyping_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="nf-core-hlatyping_logo.png" +Content-Disposition: inline; filename="nf-core-hlatyping_logo_light.png" -<% out << new File("$baseDir/assets/nf-core-hlatyping_logo.png"). - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' ) %> +<% out << new File("$projectDir/assets/nf-core-hlatyping_logo_light.png"). + bytes. + encodeBase64(). + toString(). + tokenize( '\n' )*. + toList()*. + collate( 76 )*. + collect { it.join() }. + flatten(). + join( '\n' ) %> <% if (mqcFile){ @@ -37,15 +37,15 @@ Content-ID: Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" ${mqcFileObj. - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' )} + bytes. + encodeBase64(). + toString(). + tokenize( '\n' )*. + toList()*. + collate( 76 )*. + collect { it.join() }. + flatten(). + join( '\n' )} """ }} %> diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py new file mode 100755 index 0000000..9332cdb --- /dev/null +++ b/bin/check_samplesheet.py @@ -0,0 +1,278 @@ +#!/usr/bin/env python + + +"""Provide a command line tool to validate and transform tabular samplesheets.""" + + +import argparse +import csv +import logging +import sys +from collections import Counter +from pathlib import Path + +logger = logging.getLogger() + + +class RowChecker: + """ + Define a service that can validate and transform each given row. + + Attributes: + modified (list): A list of dicts, where each dict corresponds to a previously + validated and transformed row. The order of rows is maintained. + + """ + + VALID_FORMATS = (".fq.gz", ".fastq.gz", ".fq", ".fastq", ".bam") + + def __init__( + self, + sample_col="sample", + first_col="fastq_1", + second_col="fastq_2", + single_col="single_end", + bam_col="bam", + **kwargs, + ): + """ + Initialize the row checker with the expected column names. + + Args: + sample_col (str): The name of the column that contains the sample name + (default "sample"). + first_col (str): The name of the column that contains the first (or only) + FASTQ file path (default "fastq_1"). + second_col (str): The name of the column that contains the second (if any) + FASTQ file path (default "fastq_2"). + single_col (str): The name of the new column that will be inserted and + records whether the sample contains single- or paired-end sequencing + reads (default "single_end"). + + """ + super().__init__(**kwargs) + self._sample_col = sample_col + self._first_col = first_col + self._second_col = second_col + self._single_col = single_col + self._bam_col = bam_col + self._seen = set() + self.modified = [] + + def validate_and_transform(self, row): + """ + Perform all validations on the given row and insert the read pairing status. + + Args: + row (dict): A mapping from column headers (keys) to elements of that row + (values). + + """ + self._validate_sample(row) + self._validate_first(row) + self._validate_second(row) + self._validate_pair(row) + self._validate_bam(row) + self._seen.add((row[self._sample_col], row[self._first_col])) + self.modified.append(row) + + def _validate_sample(self, row): + """Assert that the sample name exists and convert spaces to underscores.""" + if len(row[self._sample_col]) <= 0: + raise AssertionError("Sample input is required.") + # Sanitize samples slightly. + row[self._sample_col] = row[self._sample_col].replace(" ", "_") + + def _validate_first(self, row): + """Assert that the first FASTQ entry is non-empty and has the right format.""" + bam_provided = (self._bam_col in row) and (row[self._bam_col] != "") + if (len(row[self._first_col]) <= 0) and (not bam_provided): + raise AssertionError("At least the first FASTQ file is required.") + self._validate_fastq_format(row[self._first_col], bam_provided) + + def _validate_second(self, row): + """Assert that the second FASTQ entry has the right format if it exists.""" + if len(row[self._second_col]) > 0: + bam_provided = (self._bam_col in row) and (row[self._bam_col] != "") + self._validate_fastq_format(row[self._second_col], bam_provided) + + def _validate_pair(self, row): + """Assert that read pairs have the same file extension. Report pair status.""" + if row[self._first_col] and row[self._second_col]: + row[self._single_col] = False + first_col_suffix = Path(row[self._first_col]).suffixes[-2:] + second_col_suffix = Path(row[self._second_col]).suffixes[-2:] + if first_col_suffix != second_col_suffix: + raise AssertionError("FASTQ pairs must have the same file extensions.") + else: + row[self._single_col] = True + + def _validate_fastq_format(self, filename, bam_provided): + """Assert that a given filename has one of the expected FASTQ extensions.""" + if not any(filename.endswith(extension) for extension in self.VALID_FORMATS) and not bam_provided: + raise AssertionError( + f"The FASTQ file has an unrecognized extension: {filename}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" + ) + + def _validate_bam(self, row): + bam_provided = (self._bam_col in row) and (row[self._bam_col] != "") + """Assert that a given filename has the expected BAM extension.""" + if bam_provided and not row[self._bam_col].endswith("bam"): + raise AssertionError( + f"The BAM file has an unrecognized extension: {row[self._bam_col]}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" + ) + + def validate_unique_samples(self): + """ + Assert that the combination of sample name and FASTQ filename is unique. + + In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the + number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. + + """ + if len(self._seen) != len(self.modified): + raise AssertionError("The pair of sample name and FASTQ must be unique.") + seen = Counter() + for row in self.modified: + sample = row[self._sample_col] + seen[sample] += 1 + row[self._sample_col] = f"{sample}_T{seen[sample]}" + + +def read_head(handle, num_lines=10): + """Read the specified number of lines from the current position in the file.""" + lines = [] + for idx, line in enumerate(handle): + if idx == num_lines: + break + lines.append(line) + return "".join(lines) + + +def sniff_format(handle): + """ + Detect the tabular format. + + Args: + handle (text file): A handle to a `text file`_ object. The read position is + expected to be at the beginning (index 0). + + Returns: + csv.Dialect: The detected tabular format. + + .. _text file: + https://docs.python.org/3/glossary.html#term-text-file + + """ + peek = read_head(handle) + handle.seek(0) + sniffer = csv.Sniffer() + if not sniffer.has_header(peek): + logger.critical("The given sample sheet does not appear to contain a header.") + sys.exit(1) + dialect = sniffer.sniff(peek) + return dialect + + +def check_samplesheet(file_in, file_out): + """ + Check that the tabular samplesheet has the structure expected by nf-core pipelines. + + Validate the general shape of the table, expected columns, and each row. Also add + an additional column which records whether one or two FASTQ reads were found. + + Args: + file_in (pathlib.Path): The given tabular samplesheet. The format can be either + CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. + file_out (pathlib.Path): Where the validated and transformed samplesheet should + be created; always in CSV format. + + Example: + This function checks that the samplesheet follows the following structure, + see also the `viral recon samplesheet`_:: + + sample,fastq_1,fastq_2 + SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz + SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz + SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, + + or + sample,fastq_1,fastq_2,bam + SAMPLE_PE,,SAMPLE_PE.bam + + + .. _viral recon samplesheet: + https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv + + """ + required_columns = {"sample", "fastq_1", "fastq_2"} + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_in.open(newline="") as in_handle: + reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) + # Validate the existence of the expected header columns. + if not required_columns.issubset(reader.fieldnames): + req_cols = ", ".join(required_columns) + logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") + sys.exit(1) + # Validate each row. + checker = RowChecker() + for i, row in enumerate(reader): + try: + checker.validate_and_transform(row) + except AssertionError as error: + logger.critical(f"{str(error)} On line {i + 2}.") + sys.exit(1) + checker.validate_unique_samples() + header = list(reader.fieldnames) + header.insert(1, "single_end") + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_out.open(mode="w", newline="") as out_handle: + writer = csv.DictWriter(out_handle, header, delimiter=",") + writer.writeheader() + for row in checker.modified: + writer.writerow(row) + + +def parse_args(argv=None): + """Define and immediately parse command line arguments.""" + parser = argparse.ArgumentParser( + description="Validate and transform a tabular samplesheet.", + epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", + ) + parser.add_argument( + "file_in", + metavar="FILE_IN", + type=Path, + help="Tabular input samplesheet in CSV or TSV format.", + ) + parser.add_argument( + "file_out", + metavar="FILE_OUT", + type=Path, + help="Transformed output samplesheet in CSV format.", + ) + parser.add_argument( + "-l", + "--log-level", + help="The desired log level (default WARNING).", + choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), + default="WARNING", + ) + return parser.parse_args(argv) + + +def main(argv=None): + """Coordinate argument parsing and program execution.""" + args = parse_args(argv) + logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") + if not args.file_in.is_file(): + logger.error(f"The given input file {args.file_in} was not found!") + sys.exit(2) + args.file_out.parent.mkdir(parents=True, exist_ok=True) + check_samplesheet(args.file_in, args.file_out) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py deleted file mode 100755 index 76bde60..0000000 --- a/bin/scrape_software_versions.py +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env python -from __future__ import print_function -from collections import OrderedDict -import re - -regexes = { - 'nf-core/hlatyping': ['v_pipeline.txt', r"(\S+)"], - 'Nextflow': ['v_nextflow.txt', r"(\S+)"], - 'Samtools': ['v_samtools.txt', r"samtools (\S+)"], - 'Yara': ['v_yara.txt', r"yara_mapper version: (\S+)"], - 'Optitype': ['v_optitype.txt', r"Version: (\S+)"], - 'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"], -} - -results = OrderedDict() -results['nf-core/hlatyping'] = 'N/A' -results['Nextflow'] = 'N/A' -results['Samtools'] = 'N/A' -results['Yara'] = 'N/A' -results['Optitype'] = 'N/A' -results['MultiQC'] = 'N/A' - -# Search each file using its regex -for k, v in regexes.items(): - try: - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) - except IOError: - results[k] = False - -# Remove software set to false in results -for k in list(results): - if not results[k]: - del results[k] - -# Dump to YAML -print( - """ -id: 'software_versions' -section_name: 'nf-core/hlatyping Software Versions' -section_href: 'https://github.com/nf-core/hlatyping' -plot_type: 'html' -description: 'are collected at run time from the software output.' -data: | -
-""" -) -for k, v in results.items(): - print("
{}
{}
".format(k, v)) -print("
") - -# Write out regexes as csv file: -with open("software_versions.csv", "w") as f: - for k, v in results.items(): - f.write("{}\t{}\n".format(k, v)) diff --git a/conf/base.config b/conf/base.config index 77c6f42..8ddbfaf 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,43 +1,63 @@ /* - * ------------------------------------------------- - * nf-core/hlatyping Nextflow base config file - * ------------------------------------------------- - * A 'blank slate' config file, appropriate for general - * use on most high performace compute environments. - * Assumes that all software is installed and available - * on the PATH. Runs in `local` mode - all jobs will be - * run on the logged in environment. - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + nf-core/hlatyping Nextflow base config file +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + A 'blank slate' config file, appropriate for general use on most high performance + compute environments. Assumes that all software is installed and available on + the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. +---------------------------------------------------------------------------------------- +*/ process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 7.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { check_max( 1 * task.attempt, 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + maxRetries = 1 + maxErrors = '-1' - withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 14.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 42.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } - } - withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 84.GB * task.attempt, 'memory' ) } - time = { check_max( 10.h * task.attempt, 'time' ) } - } - withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } - } - withName:get_software_versions { - cache = false - } -} \ No newline at end of file + // Process-specific resource requirements + // NOTE - Please try and re-use the labels below as much as possible. + // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. + // If possible, it would be nice to keep the same label naming convention when + // adding in your local modules too. + // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors + withLabel:process_single { + cpus = { check_max( 1 , 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } + } + withLabel:process_low { + cpus = { check_max( 2 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } + } + withLabel:process_medium { + cpus = { check_max( 6 * task.attempt, 'cpus' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } + } + withLabel:process_high { + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { check_max( 72.GB * task.attempt, 'memory' ) } + time = { check_max( 16.h * task.attempt, 'time' ) } + } + withLabel:process_long { + time = { check_max( 20.h * task.attempt, 'time' ) } + } + withLabel:process_high_memory { + memory = { check_max( 200.GB * task.attempt, 'memory' ) } + } + withLabel:error_ignore { + errorStrategy = 'ignore' + } + withLabel:error_retry { + errorStrategy = 'retry' + maxRetries = 2 + } + withName:CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false + } +} diff --git a/conf/igenomes.config b/conf/igenomes.config index caeafce..7a1b3ac 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -1,421 +1,432 @@ /* - * ------------------------------------------------- - * Nextflow config file for iGenomes paths - * ------------------------------------------------- - * Defines reference genomes, using iGenome paths - * Can be used by any config that customises the base - * path using $params.igenomes_base / --igenomes_base - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines reference genomes using iGenome paths. + Can be used by any config that customises the base path using: + $params.igenomes_base / --igenomes_base +---------------------------------------------------------------------------------------- +*/ params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed" + // illumina iGenomes reference file paths + genomes { + 'GRCh37' { + fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" + } + 'GRCh38' { + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + 'GRCm38' { + fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" + } + 'TAIR10' { + fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" + mito_name = "Mt" + } + 'EB2' { + fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" + } + 'UMD3.1' { + fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" + mito_name = "MT" + } + 'WBcel235' { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" + mito_name = "MtDNA" + macs_gsize = "9e7" + } + 'CanFam3.1' { + fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" + mito_name = "MT" + } + 'GRCz10' { + fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'BDGP6' { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" + mito_name = "M" + macs_gsize = "1.2e8" + } + 'EquCab2' { + fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" + mito_name = "MT" + } + 'EB1' { + fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" + } + 'Galgal4' { + fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'Gm01' { + fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" + } + 'Mmul_1' { + fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" + mito_name = "MT" + } + 'IRGSP-1.0' { + fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" + mito_name = "Mt" + } + 'CHIMP2.1.4' { + fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" + mito_name = "MT" + } + 'Rnor_5.0' { + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'Rnor_6.0' { + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" + mito_name = "MT" + } + 'R64-1-1' { + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" + mito_name = "MT" + macs_gsize = "1.2e7" + } + 'EF2' { + fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.21e7" + } + 'Sbi1' { + fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" + } + 'Sscrofa10.2' { + fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" + mito_name = "MT" + } + 'AGPv3' { + fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" + mito_name = "Mt" + } + 'hg38' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + 'hg19' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" + } + 'mm10' { + fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" + } + 'bosTau8' { + fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + 'ce10' { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "9e7" + } + 'canFam3' { + fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" + mito_name = "chrM" + } + 'danRer10' { + fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "1.37e9" + } + 'dm6' { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "1.2e8" + } + 'equCab2' { + fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" + mito_name = "chrM" + } + 'galGal4' { + fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" + mito_name = "chrM" + } + 'panTro4' { + fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" + mito_name = "chrM" + } + 'rn6' { + fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + 'sacCer3' { + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" + readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.2e7" + } + 'susScr3' { + fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" + mito_name = "chrM" + } } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${baseDir}/assets/blacklists/hg38-blacklist.bed" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${baseDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${baseDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${baseDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${baseDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } } diff --git a/conf/modules.config b/conf/modules.config new file mode 100644 index 0000000..7b9a0ba --- /dev/null +++ b/conf/modules.config @@ -0,0 +1,62 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. +---------------------------------------------------------------------------------------- +*/ + +process { + + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + withName: SAMPLESHEET_CHECK { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: CHECK_PAIRED { + ext.args = '' + } + + withName: FASTQC { + ext.args = '--quiet' + } + + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } + + withName: YARA_MAPPER { + ext.args = '-e 3' + publishDir = [ + path: { "${params.outdir}/yara/${meta.id}" }, + mode: params.publish_dir_mode + ] + } + + withName: OPTITYPE { + publishDir = [ + path: { "${params.outdir}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + ext.args2 = "solver=${params.solver}" + } + +} diff --git a/conf/test.config b/conf/test.config index 75f505d..67a222e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,26 +1,25 @@ /* - * ------------------------------------------------- - * Nextflow config file for running tests - * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a fast and simple test. Use as follows: - * nextflow run nf-core/hlatyping -profile test, - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h + // Limit resources so that this can run on GitHub Actions + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' - // Input data - single_end = false - input = 'https://github.com/nf-core/test-datasets/raw/hlatyping/bam/example_pe.bam' - solver = 'glpk' - seqtype = 'dna' - bam = true - outdir = 'results' -} \ No newline at end of file + // Input data + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/hlatyping/samplesheets/samplesheet_bam.csv' + solver = 'glpk' +} diff --git a/conf/test_dna_rna.config b/conf/test_dna_rna.config new file mode 100644 index 0000000..311573b --- /dev/null +++ b/conf/test_dna_rna.config @@ -0,0 +1,22 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running fastq tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines bundled input files and everything required to run a fast and simple test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test_dna_rna, --outdir +---------------------------------------------------------------------------------------- + */ + +params { + config_profile_name = 'fastq (DNA/RNA) Test Profile' + config_profile_description = 'Test dataset with paired-end fastq files from DNA and RNA' + + max_cpus = 2 + max_memory = '6.GB' + max_time = '48.h' + + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/hlatyping/samplesheets/samplesheet_dna_rna.csv' + solver = 'glpk' +} diff --git a/conf/test_fastq.config b/conf/test_fastq.config index 990c051..616288e 100644 --- a/conf/test_fastq.config +++ b/conf/test_fastq.config @@ -1,24 +1,22 @@ /* - * ------------------------------------------------- - * Nextflow config file for running tests - * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a fast and simple test. Use as follows: - * nextflow run nf-core/hlatyping -profile test +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running fastq tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines bundled input files and everything required to run a fast and simple test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test, --outdir +---------------------------------------------------------------------------------------- */ params { - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - single_end = false - input_paths = [ - ['Testdata', ['https://github.com/nf-core/test-datasets/raw/hlatyping/fastq/NA11995_SRR766010_1_fished.fastq.gz', - 'https://github.com/nf-core/test-datasets/raw/hlatyping/fastq/NA11995_SRR766010_2_fished.fastq.gz']] - ] - solver = 'glpk' - seqtype = 'dna' - bam = false - index = "$baseDir/data/indices/yara/hla_reference_dna" - outdir = "results" -} \ No newline at end of file + config_profile_name = 'fastq Test Profile' + config_profile_description = 'Test dataset with paired-end fastq files (DNA)' + + max_cpus = 2 + max_memory = '6.GB' + max_time = '48.h' + + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/hlatyping/samplesheets/samplesheet_fastq.csv' + solver = 'glpk' +} diff --git a/conf/test_full.config b/conf/test_full.config index b6b70fa..638e061 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -1,24 +1,21 @@ /* - * ------------------------------------------------- - * Nextflow config file for running full-size tests - * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a full size pipeline test. Use as follows: - * nextflow run nf-core/hlatyping -profile test_full, - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running full-size tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a full size pipeline test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test_full, --outdir + +---------------------------------------------------------------------------------------- +*/ params { - config_profile_name = 'Full test profile' - config_profile_description = 'Full test dataset to check pipeline function' + config_profile_name = 'Full test profile' + config_profile_description = 'Full test dataset (fastq and bam files) to check pipeline function' + + // Input data for full size test + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/hlatyping/samplesheets/samplesheet_full.csv' + solver = 'glpk' - // Input data for full size test - single_end = false - input_paths = [ - ['Testdata', ['ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR795/SRR795091/SRR795091_1.fastq.gz', - 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR795/SRR795091/SRR795091_2.fastq.gz']] - ] - solver = 'glpk' - seqtype = 'dna' - bam = false - outdir = "results" } diff --git a/conf/test_rna.config b/conf/test_rna.config index 449d6b0..30f08b3 100644 --- a/conf/test_rna.config +++ b/conf/test_rna.config @@ -1,23 +1,22 @@ /* - * ------------------------------------------------- - * Nextflow config file for running tests - * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a fast and simple test. Use as follows: - * nextflow run nf-core/hlatyping -profile test - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines bundled input files and everything required to run a fast and simple test. + + Use as follows: + nextflow run nf-core/hlatyping -profile test_rna, --outdir + +---------------------------------------------------------------------------------------- +*/ params { - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - single_end = false - input_paths = [ - ['Testdata', ['https://github.com/nf-core/test-datasets/raw/hlatyping/rna/CRC_81_N_1_fished.fastq.gz', - 'https://github.com/nf-core/test-datasets/raw/hlatyping/rna/CRC_81_N_2_fished.fastq.gz']] - ] - solver = 'glpk' - seqtype = 'rna' - bam = false - outdir = "results" + config_profile_name = 'RNA Test Profile' + config_profile_description = 'RNA fastq test dataset' + + max_cpus = 2 + max_memory = '6.GB' + max_time = '48.h' + + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/hlatyping/samplesheets/samplesheet_rna.csv' } diff --git a/data/indices/yara/hla_reference_dna.lf.drp b/data/indices/yara/hla_reference_dna.lf.drp deleted file mode 100644 index a9cf647..0000000 Binary files a/data/indices/yara/hla_reference_dna.lf.drp and /dev/null differ diff --git a/data/indices/yara/hla_reference_dna.lf.drs b/data/indices/yara/hla_reference_dna.lf.drs deleted file mode 100644 index fc2b569..0000000 --- a/data/indices/yara/hla_reference_dna.lf.drs +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/data/indices/yara/hla_reference_dna.lf.drv b/data/indices/yara/hla_reference_dna.lf.drv deleted file mode 100644 index c280370..0000000 Binary files a/data/indices/yara/hla_reference_dna.lf.drv and /dev/null differ diff --git a/data/indices/yara/hla_reference_dna.lf.pst b/data/indices/yara/hla_reference_dna.lf.pst deleted file mode 100644 index 59e7d29..0000000 Binary files a/data/indices/yara/hla_reference_dna.lf.pst and /dev/null differ diff --git a/data/indices/yara/hla_reference_dna.rid.concat b/data/indices/yara/hla_reference_dna.rid.concat deleted file mode 100644 index 59a2b2a..0000000 --- a/data/indices/yara/hla_reference_dna.rid.concat +++ /dev/null @@ -1 +0,0 @@ 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097HLA09412_HLA00104HLA09413_HLA00115HLA09413_HLA05918HLA09414_HLA00001HLA09414_HLA02169HLA09415_HLA00001HLA09415_HLA02169HLA09416_HLA00001HLA09416_HLA02169HLA09417_HLA00001HLA09417_HLA02169HLA09418_HLA00037HLA09418_HLA01960HLA09419_HLA00037HLA09419_HLA01960HLA09420_HLA00037HLA09420_HLA01960HLA09421_HLA00010HLA09422_HLA00005HLA09422_HLA03253HLA09422_HLA01218HLA09447_HLA00097HLA09458_HLA00050HLA09458_HLA00051HLA09458_HLA06112HLA09463_HLA00005HLA09463_HLA03253HLA09465_HLA00089HLA09466_HLA00003HLA09468_HLA00005HLA09468_HLA03253HLA09469_HLA00037HLA09469_HLA01960HLA09474_HLA00073HLA09479_HLA00073HLA09480_HLA00043HLA09481_HLA00005HLA09481_HLA03253HLA09484_HLA00043HLA09485_HLA00050HLA09485_HLA00051HLA09485_HLA06112HLA09486_HLA00011HLA09490_HLA00073HLA09492_HLA00073HLA09494_HLA00011HLA09495_HLA00050HLA09495_HLA00051HLA09495_HLA06112HLA09496_HLA00043HLA09497_HLA00040HLA09498_HLA00050HLA09498_HLA00051HLA09498_HLA06112HLA09499_HLA00073HLA09506_HLA00001HLA09506_HLA02169HLA09508_HLA00043HLA09510_HLA00073HLA09514_HLA00037HLA09514_HLA01960HLA09516_HLA00005HLA09516_HLA03253HLA09516_HLA01218HLA09520_HLA00086HLA09521_HLA00104HLA09522_HLA00106HLA09523_HLA00043HLA09524_HLA00073HLA09525_HLA00073HLA09526_HLA00073HLA09527_HLA00090HLA09528_HLA00089HLA09529_HLA00090HLA09530_HLA00048HLA09531_HLA00050HLA09531_HLA00051HLA09531_HLA06112HLA09532_HLA00050HLA09532_HLA00051HLA09532_HLA06112HLA09533_HLA00050HLA09533_HLA00051HLA09533_HLA06112HLA09534_HLA00050HLA09534_HLA00051HLA09534_HLA06112HLA09535_HLA00050HLA09535_HLA00051HLA09535_HLA06112HLA09536_HLA00050HLA09536_HLA00051HLA09536_HLA06112HLA09537_HLA00001HLA09537_HLA02169HLA09538_HLA00001HLA09538_HLA02169HLA09539_HLA00001HLA09539_HLA02169HLA09540_HLA00037HLA09540_HLA01960HLA09541_HLA00037HLA09541_HLA01960HLA09542_HLA00037HLA09542_HLA01960HLA09543_HLA00037HLA09543_HLA01960HLA09544_HLA00101HLA09545_HLA00037HLA09545_HLA01960HLA09546_HLA00037HLA09546_HLA01960HLA09547_HLA00090HLA09548_HLA00010HLA09549_HLA00005HLA09549_HLA03253HLA09549_HLA01218HLA09550_HLA00005HLA09550_HLA03253HLA09550_HLA01218HLA09551_HLA00005HLA09551_HLA03253HLA09551_HLA01218HLA09552_HLA00005HLA09552_HLA03253HLA09552_HLA01218HLA09553_HLA00005HLA09553_HLA03253HLA09553_HLA01218HLA09568_HLA00112HLA09659_HLA00116HLA09662_HLA00008HLA09682_HLA00043HLA09692_HLA00012HLA09693_HLA00005HLA09693_HLA03253HLA09693_HLA01218HLA09705_HLA00089HLA09707_HLA00037HLA09707_HLA01960HLA09712_HLA00115HLA09712_HLA05918HLA09715_HLA00008HLA09718_HLA00012HLA09774_HLA00043HLA09775_HLA00106HLA09776_HLA00097HLA09777_HLA00097HLA09778_HLA00097HLA09779_HLA00106HLA09780_HLA00044HLA09781_HLA00043HLA09782_HLA00043HLA09783_HLA00071HLA09784_HLA00073HLA09785_HLA00126HLA09786_HLA00117HLA09786_HLA02911HLA09787_HLA00115HLA09787_HLA05918HLA09788_HLA00043HLA09789_HLA00116HLA09790_HLA00050HLA09790_HLA00051HLA09790_HLA06112HLA09791_HLA00050HLA09791_HLA00051HLA09791_HLA06112HLA09792_HLA00050HLA09792_HLA00051HLA09792_HLA06112HLA09793_HLA00050HLA09793_HLA00051HLA09793_HLA06112HLA09794_HLA00048HLA09795_HLA00050HLA09795_HLA00051HLA09795_HLA06112HLA09796_HLA00050HLA09796_HLA00051HLA09796_HLA06112HLA09797_HLA00050HLA09797_HLA00051HLA09797_HLA06112HLA09798_HLA00050HLA09798_HLA00051HLA09798_HLA06112HLA09799_HLA00001HLA09799_HLA02169HLA09800_HLA00001HLA09800_HLA02169HLA09801_HLA00001HLA09801_HLA02169HLA09802_HLA02057HLA09803_HLA00001HLA09803_HLA02169HLA09804_HLA00037HLA09804_HLA01960HLA09805_HLA00037HLA09805_HLA01960HLA09806_HLA00037HLA09806_HLA01960HLA09807_HLA00073HLA09808_HLA00010HLA09809_HLA00005HLA09809_HLA03253HLA09809_HLA01218HLA09810_HLA00005HLA09810_HLA03253HLA09810_HLA01218HLA09811_HLA00005HLA09811_HLA03253HLA09811_HLA01218HLA09812_HLA00005HLA09812_HLA03253HLA09812_HLA01218HLA09813_HLA00005HLA09813_HLA03253HLA09813_HLA01218HLA09814_HLA00005HLA09814_HLA03253HLA09814_HLA01218HLA09815_HLA00005HLA09815_HLA03253HLA09815_HLA01218HLA09816_HLA00005HLA09816_HLA03253HLA09816_HLA01218HLA09817_HLA00005HLA09817_HLA03253HLA09817_HLA01218HLA09824_HLA00085HLA09824_HLA01406HLA09825_HLA00050HLA09825_HLA00051HLA09825_HLA06112HLA09877_HLA00011HLA09878_HLA00050HLA09878_HLA00051HLA09878_HLA06112HLA00132HLA00137HLA01742HLA02164HLA02560HLA00146HLA00975HLA01717HLA01752HLA02849HLA07386HLA00152HLA00153HLA02295HLA01476HLA02389HLA03834HLA00158HLA02166HLA00162HLA00165HLA00166HLA00167HLA00170HLA02376HLA00173HLA00174HLA00176HLA00179HLA00180HLA01439HLA00181HLA00188HLA00190HLA00195HLA00205HLA01118HLA01440HLA01743HLA01845HLA00213HLA07768HLA00214HLA00215HLA01532HLA02851HLA00223HLA00225HLA00227HLA00228HLA01504HLA01529HLA02370HLA00237HLA05817HLA00238HLA00239HLA00241HLA00244HLA01741HLA01563HLA00265HLA03651HLA00267HLA00268HLA02584HLA00271HLA09085HLA00278HLA00280HLA00284HLA02165HLA02163HLA02412HLA00291HLA00293HLA00294HLA00297HLA01430HLA00301HLA01510HLA02850HLA03160HLA00312HLA00315HLA00316HLA02390HLA00318HLA08401HLA06304HLA00319HLA00320HLA00321HLA00326HLA07343HLA07767HLA01341HLA02343HLA02675HLA03130HLA00329HLA01343HLA00331HLA05818HLA00332HLA01437HLA00335HLA00337HLA00338HLA01777HLA00340HLA00341HLA00344HLA00345HLA00346HLA00352HLA02558HLA00362HLA00364HLA02352HLA00367HLA03748HLA00368HLA00369HLA01553HLA02677HLA05807HLA00376HLA00378HLA00379HLA00381HLA00383HLA01074HLA02676HLA00386HLA00389HLA00390HLA00391HLA01374HLA00392HLA00393HLA00398HLA01188HLA00133_HLA00132HLA00134_HLA00132HLA00135_HLA02560HLA00136_HLA00132HLA00139_HLA00132HLA00140_HLA02560HLA00141_HLA00132HLA00142_HLA00132HLA00143_HLA00132HLA00144_HLA00132HLA00145_HLA00132HLA00147_HLA00146HLA00148_HLA00146HLA00148_HLA01717HLA00149_HLA00146HLA00149_HLA01717HLA00150_HLA00146HLA00150_HLA01717HLA00154_HLA00153HLA00155_HLA05413HLA00157_HLA00158HLA00157_HLA02166HLA00159_HLA00158HLA00160_HLA00158HLA00161_HLA00158HLA00164_HLA00162HLA00168_HLA00162HLA00169_HLA00190HLA00171_HLA00174HLA00172_HLA00173HLA00175_HLA00162HLA00177_HLA00162HLA00178_HLA00174HLA00183_HLA00188HLA00184_HLA00165HLA00185_HLA00174HLA00186_HLA00181HLA00187_HLA00162HLA00189_HLA00162HLA00191_HLA00162HLA00192_HLA00181HLA00193_HLA01118HLA00194_HLA00165HLA00194_HLA00174HLA00196_HLA00162HLA00197_HLA00162HLA00198_HLA00162HLA00199_HLA00176HLA00200_HLA00173HLA00201_HLA00162HLA00202_HLA00162HLA00203_HLA00162HLA00206_HLA00162HLA00207_HLA00165HLA00208_HLA00170HLA00209_HLA00162HLA00210_HLA00166HLA00211_HLA01118HLA00212_HLA00166HLA00216_HLA00213HLA00216_HLA07768HLA00216_HLA01532HLA00217_HLA00213HLA00217_HLA07768HLA00217_HLA01532HLA00218_HLA00213HLA00218_HLA07768HLA00219_HLA00213HLA00219_HLA07768HLA00219_HLA01532HLA00220_HLA00225HLA00221_HLA00225HLA00222_HLA00225HLA00226_HLA00225HLA00229_HLA00223HLA00229_HLA00225HLA00230_HLA00225HLA00231_HLA00225HLA00232_HLA00228HLA00233_HLA00223HLA00233_HLA00225HLA00235_HLA00225HLA00236_HLA00223HLA00240_HLA00238HLA00242_HLA00239HLA00243_HLA00237HLA00245_HLA00238HLA00246_HLA00238HLA00247_HLA00237HLA00248_HLA00237HLA00249_HLA00238HLA00250_HLA00239HLA00251_HLA01741HLA00252_HLA00237HLA00253_HLA00237HLA00254_HLA00237HLA00255_HLA00238HLA00256_HLA00237HLA00257_HLA00237HLA00258_HLA00237HLA00259_HLA00241HLA00260_HLA00237HLA00261_HLA00237HLA00262_HLA00237HLA00263_HLA00237HLA00264_HLA00237HLA00266_HLA00225HLA00269_HLA00268HLA00270_HLA00268HLA00274_HLA00273HLA00274_HLA02165HLA00275_HLA02165HLA00276_HLA00271HLA00277_HLA00271HLA00279_HLA00280HLA00281_HLA00278HLA00282_HLA02165HLA00283_HLA00271HLA00285_HLA00278HLA00286_HLA00271HLA00287_HLA02165HLA00288_HLA00271HLA00289_HLA00271HLA00290_HLA00284HLA00295_HLA00293HLA00296_HLA00293HLA00298_HLA00292HLA00299_HLA00293HLA00300_HLA00293HLA00302_HLA00293HLA00303_HLA00301HLA00303_HLA00337HLA00304_HLA00293HLA00305_HLA02850HLA00306_HLA00291HLA00307_HLA00292HLA00309_HLA00293HLA00310_HLA00293HLA00311_HLA00294HLA00313_HLA00312HLA00314_HLA00312HLA00322_HLA00318HLA00322_HLA08401HLA00323_HLA02558HLA00324_HLA00320HLA00325_HLA00318HLA00325_HLA08401HLA00327_HLA00320HLA00328_HLA00318HLA00328_HLA08401HLA00330_HLA00329HLA00333_HLA00332HLA00333_HLA01437HLA00334_HLA00332HLA00334_HLA01437HLA00336_HLA00166HLA00336_HLA00237HLA00336_HLA02165HLA00339_HLA01777HLA00342_HLA00341HLA00347_HLA00345HLA00348_HLA00344HLA00349_HLA00344HLA00350_HLA00345HLA00351_HLA00344HLA00353_HLA00344HLA00354_HLA00344HLA00355_HLA00346HLA00357_HLA00344HLA00358_HLA00344HLA00359_HLA00344HLA00360_HLA00345HLA00361_HLA00344HLA00363_HLA00362HLA00365_HLA00364HLA00366_HLA00364HLA00370_HLA00368HLA00371_HLA00379HLA00372_HLA00368HLA00374_HLA00369HLA00375_HLA00379HLA00377_HLA00379HLA00380_HLA00376HLA00382_HLA00383HLA00384_HLA00381HLA00385_HLA00383HLA00387_HLA00386HLA00394_HLA00393HLA00395_HLA00393HLA00396_HLA00393HLA00399_HLA01188HLA00974_HLA00146HLA00974_HLA01717HLA00976_HLA00146HLA00977_HLA00158HLA00978_HLA00162HLA00979_HLA00162HLA00980_HLA00181HLA00981_HLA00237HLA00982_HLA00237HLA00983_HLA00301HLA00984_HLA00291HLA00986_HLA00335HLA00987_HLA00364HLA00988_HLA00393HLA00989_HLA00376HLA00990_HLA00393HLA01049_HLA00132HLA01050_HLA00132HLA01051_HLA02560HLA01052_HLA00158HLA01053_HLA00181HLA01054_HLA00162HLA01055_HLA00213HLA01055_HLA07768HLA01055_HLA01532HLA01056_HLA00225HLA01057_HLA00237HLA01058_HLA00241HLA01059_HLA00241HLA01060_HLA00239HLA01061_HLA00284HLA01062_HLA00292HLA01063_HLA00293HLA01064_HLA00291HLA01065_HLA00318HLA01065_HLA08401HLA01066_HLA00319HLA01067_HLA00318HLA01067_HLA08401HLA01068_HLA00329HLA01068_HLA00340HLA01069_HLA00335HLA01070_HLA00341HLA01071_HLA00344HLA01072_HLA00344HLA01073_HLA00344HLA01082_HLA00146HLA01082_HLA01717HLA01103_HLA00166HLA01110_HLA00132HLA01113_HLA00165HLA01113_HLA00174HLA01114_HLA00162HLA01116_HLA00132HLA01117_HLA00162HLA01122_HLA00293HLA01123_HLA00271HLA01126_HLA00344HLA01127_HLA00344HLA01128_HLA00271HLA01129_HLA00293HLA01130_HLA00225HLA01131_HLA00213HLA01131_HLA07768HLA01131_HLA01532HLA01132_HLA00344HLA01133_HLA00271HLA01134_HLA00344HLA01135_HLA00378HLA01137_HLA00268HLA01139_HLA00331HLA01140_HLA02343HLA01141_HLA00362HLA01142_HLA00386HLA01143_HLA00223HLA01144_HLA00340HLA01146_HLA00318HLA01146_HLA08401HLA01147_HLA02370HLA01148_HLA00318HLA01148_HLA08401HLA01149_HLA00344HLA01173_HLA01504HLA01176_HLA00315HLA01177_HLA00213HLA01177_HLA07768HLA01177_HLA01532HLA01178_HLA00364HLA01180_HLA02677HLA01181_HLA00386HLA01182_HLA00174HLA01183_HLA00284HLA01184_HLA00132HLA01192_HLA00383HLA01193_HLA00146HLA01193_HLA01717HLA01194_HLA00237HLA01195_HLA00318HLA01195_HLA08401HLA01196_HLA00271HLA01197_HLA00318HLA01197_HLA08401HLA01200_HLA00162HLA01201_HLA00174HLA01202_HLA00237HLA01203_HLA02165HLA01204_HLA00367HLA01205_HLA00369HLA01219_HLA00267HLA01221_HLA00271HLA01223_HLA00293HLA01229_HLA00329HLA01230_HLA00146HLA01230_HLA01717HLA01231_HLA00362HLA01232_HLA00291HLA01243_HLA00344HLA01245_HLA00346HLA01246_HLA00291HLA01247_HLA00318HLA01247_HLA08401HLA01250_HLA00166HLA01252_HLA00340HLA01253_HLA00132HLA01256_HLA00312HLA01257_HLA00132HLA01261_HLA00364HLA01262_HLA00344HLA01264_HLA00237HLA01265_HLA00267HLA01266_HLA00340HLA01266_HLA00362HLA01267_HLA00265HLA01269_HLA00291HLA01270_HLA00213HLA01270_HLA07768HLA01270_HLA01532HLA01271_HLA00166HLA01276_HLA00152HLA01277_HLA00227HLA01281_HLA00213HLA01281_HLA07768HLA01281_HLA01532HLA01284_HLA00162HLA01285_HLA00181HLA01286_HLA00132HLA01287_HLA00291HLA01288_HLA00312HLA01289_HLA00383HLA01293_HLA00132HLA01294_HLA00267HLA01295_HLA00362HLA01296_HLA00239HLA01299_HLA00291HLA01309_HLA00152HLA01312_HLA00386HLA01313_HLA00318HLA01313_HLA08401HLA01314_HLA00237HLA01319_HLA00364HLA01329_HLA00293HLA01346_HLA00265HLA01348_HLA00223HLA01352_HLA00146HLA01352_HLA01717HLA01353_HLA00213HLA01353_HLA07768HLA01353_HLA01532HLA01354_HLA00318HLA01354_HLA08401HLA01358_HLA00132HLA01359_HLA00265HLA01362_HLA00132HLA01373_HLA00162HLA01403_HLA00393HLA01417_HLA00344HLA01418_HLA00146HLA01418_HLA01717HLA01419_HLA00329HLA01426_HLA00162HLA01427_HLA00318HLA01427_HLA08401HLA01435_HLA02560HLA01448_HLA00179HLA01449_HLA00319HLA01450_HLA00291HLA01452_HLA00312HLA01461_HLA00381HLA01474_HLA00344HLA01479_HLA00166HLA01481_HLA00332HLA01481_HLA01437HLA01482_HLA00291HLA01484_HLA00364HLA01485_HLA00383HLA01486_HLA00205HLA01487_HLA00318HLA01487_HLA08401HLA01488_HLA00293HLA01490_HLA00291HLA01493_HLA00271HLA01494_HLA00166HLA01495_HLA00293HLA01503_HLA00239HLA01506_HLA00213HLA01506_HLA07768HLA01506_HLA01532HLA01507_HLA00368HLA01508_HLA00213HLA01508_HLA07768HLA01508_HLA01532HLA01509_HLA00237HLA01515_HLA00268HLA01516_HLA00132HLA01520_HLA00381HLA01521_HLA00320HLA01522_HLA02352HLA01524_HLA00315HLA01526_HLA00319HLA01527_HLA00291HLA01528_HLA00271HLA01530_HLA00319HLA01535_HLA00146HLA01535_HLA01717HLA01536_HLA00162HLA01537_HLA00344HLA01548_HLA00132HLA01561_HLA00162HLA01564_HLA00376HLA01565_HLA00213HLA01565_HLA07768HLA01565_HLA01532HLA01567_HLA00181HLA01568_HLA00344HLA01569_HLA07767HLA01577_HLA00132HLA01580_HLA00362HLA01591_HLA00152HLA01600_HLA00291HLA01604_HLA00297HLA01604_HLA01430HLA01607_HLA00329HLA01611_HLA01118HLA01613_HLA00213HLA01613_HLA07768HLA01613_HLA01532HLA01617_HLA00319HLA01618_HLA00132HLA01625_HLA00379HLA01626_HLA00344HLA01627_HLA00362HLA01632_HLA00152HLA01635_HLA00225HLA01641_HLA00146HLA01641_HLA01717HLA01642_HLA00225HLA01654_HLA00146HLA01655_HLA00267HLA01656_HLA00271HLA01658_HLA00379HLA01667_HLA02850HLA01668_HLA00244HLA01676_HLA00344HLA01677_HLA00362HLA01678_HLA00346HLA01679_HLA00166HLA01680_HLA00386HLA01688_HLA00379HLA01690_HLA00162HLA01691_HLA00318HLA01691_HLA08401HLA01698_HLA00174HLA01698_HLA00378HLA01700_HLA00318HLA01700_HLA08401HLA01701_HLA00146HLA01701_HLA01717HLA01702_HLA00291HLA01712_HLA00315HLA01713_HLA00318HLA01713_HLA08401HLA01719_HLA00376HLA01722_HLA00369HLA01723_HLA00386HLA01725_HLA02560HLA01727_HLA00237HLA01728_HLA00386HLA01732_HLA00368HLA01740_HLA00291HLA01748_HLA00291HLA01749_HLA00368HLA01750_HLA00137HLA01751_HLA00162HLA01763_HLA00132HLA01764_HLA00379HLA01765_HLA00291HLA01767_HLA00162HLA01768_HLA00181HLA01772_HLA00146HLA01772_HLA01717HLA01782_HLA00213HLA01782_HLA07768HLA01782_HLA01532HLA01783_HLA00132HLA01784_HLA00319HLA01788_HLA00369HLA01789_HLA00271HLA01790_HLA00319HLA01792_HLA00162HLA01797_HLA00319HLA01800_HLA00291HLA01801_HLA00162HLA01804_HLA00319HLA01808_HLA00132HLA01816_HLA00291HLA01840_HLA00152HLA01846_HLA00237HLA01850_HLA00237HLA01858_HLA00152HLA01881_HLA02560HLA01883_HLA02560HLA01888_HLA00237HLA01892_HLA00376HLA01896_HLA00237HLA01897_HLA00241HLA01898_HLA00291HLA01899_HLA00293HLA01900_HLA00190HLA01911_HLA00188HLA01912_HLA00205HLA01913_HLA00162HLA01914_HLA00213HLA01914_HLA07768HLA01915_HLA00165HLA01916_HLA00176HLA01917_HLA00146HLA01917_HLA01717HLA01919_HLA00292HLA01920_HLA00271HLA01921_HLA00291HLA01922_HLA00364HLA01923_HLA00267HLA01924_HLA00271HLA01926_HLA00271HLA01927_HLA00271HLA01939_HLA00315HLA01941_HLA00315HLA01949_HLA00265HLA01950_HLA00173HLA01951_HLA00166HLA01952_HLA00223HLA01953_HLA00332HLA01953_HLA01437HLA01964_HLA00362HLA01975_HLA00162HLA01976_HLA00291HLA01977_HLA00331HLA01979_HLA00297HLA01979_HLA01430HLA01980_HLA00331HLA01982_HLA00335HLA01983_HLA00344HLA01984_HLA00237HLA01985_HLA00225HLA01986_HLA00319HLA01989_HLA00181HLA01990_HLA00237HLA01992_HLA00291HLA01995_HLA00293HLA01996_HLA00293HLA01999_HLA00162HLA02002_HLA00376HLA02003_HLA00346HLA02004_HLA00386HLA02007_HLA01777HLA02015_HLA00265HLA02016_HLA00237HLA02020_HLA00344HLA02023_HLA00228HLA02027_HLA00367HLA02031_HLA00239HLA02032_HLA00179HLA02035_HLA00162HLA02038_HLA00239HLA02043_HLA00376HLA02077_HLA00297HLA02077_HLA01430HLA02078_HLA00364HLA02079_HLA00378HLA02089_HLA00132HLA02092_HLA00368HLA02093_HLA00205HLA02093_HLA00369HLA02095_HLA00367HLA02096_HLA00367HLA02097_HLA02163HLA02098_HLA00318HLA02098_HLA08401HLA02099_HLA00162HLA02100_HLA00225HLA02104_HLA00335HLA02112_HLA00335HLA02113_HLA00166HLA02114_HLA00364HLA02117_HLA00344HLA02118_HLA00225HLA02119_HLA00173HLA02122_HLA00369HLA02128_HLA00241HLA02129_HLA00137HLA02132_HLA00146HLA02132_HLA01717HLA02134_HLA00239HLA02137_HLA00368HLA02140_HLA00331HLA02141_HLA00180HLA02141_HLA01439HLA02142_HLA00146HLA02142_HLA01717HLA02143_HLA00238HLA02144_HLA00312HLA02149_HLA00265HLA02150_HLA00158HLA02161_HLA00267HLA02167_HLA00344HLA02171_HLA00225HLA02174_HLA00153HLA02175_HLA00132HLA02176_HLA00237HLA02179_HLA00367HLA02200_HLA00338HLA02206_HLA00318HLA02206_HLA08401HLA02209_HLA00340HLA02211_HLA00331HLA02212_HLA00362HLA02217_HLA01510HLA02218_HLA00225HLA02219_HLA00146HLA02219_HLA01717HLA02227_HLA00292HLA02228_HLA00205HLA02228_HLA00393HLA02229_HLA00292HLA02231_HLA00265HLA02234_HLA00319HLA02238_HLA02370HLA02246_HLA00223HLA02247_HLA00132HLA02249_HLA00291HLA02251_HLA00244HLA02252_HLA00146HLA02252_HLA01717HLA02259_HLA00381HLA02260_HLA00238HLA02261_HLA00376HLA02262_HLA00293HLA02296_HLA00301HLA02297_HLA00344HLA02298_HLA00331HLA02300_HLA00291HLA02301_HLA00223HLA02307_HLA00381HLA02308_HLA00146HLA02308_HLA01717HLA02309_HLA00318HLA02309_HLA08401HLA02311_HLA00146HLA02311_HLA01717HLA02311_HLA00315HLA02313_HLA00237HLA02315_HLA00213HLA02315_HLA07768HLA02315_HLA01532HLA02316_HLA00319HLA02317_HLA00137HLA02320_HLA00369HLA02329_HLA00137HLA02330_HLA00162HLA02331_HLA00271HLA02332_HLA00188HLA02335_HLA00368HLA02336_HLA00331HLA02342_HLA00340HLA02360_HLA00153HLA02368_HLA00162HLA02377_HLA00335HLA02378_HLA00271HLA02383_HLA00291HLA02384_HLA00278HLA02385_HLA00244HLA02387_HLA00190HLA02388_HLA00213HLA02388_HLA07768HLA02388_HLA01532HLA02393_HLA00132HLA02394_HLA00267HLA02398_HLA00367HLA02399_HLA00237HLA02400_HLA00146HLA02400_HLA01717HLA02402_HLA00237HLA02406_HLA00146HLA02406_HLA01717HLA02407_HLA00369HLA02411_HLA00239HLA02418_HLA00265HLA02419_HLA00346HLA02421_HLA00162HLA02426_HLA00271HLA02436_HLA00271HLA02437_HLA00228HLA02437_HLA01504HLA02446_HLA00132HLA02452_HLA00362HLA02454_HLA00162HLA02455_HLA00344HLA02457_HLA00271HLA02458_HLA00291HLA02463_HLA00132HLA02464_HLA00320HLA02465_HLA00165HLA02473_HLA00228HLA02477_HLA00267HLA02479_HLA00265HLA02480_HLA00241HLA02482_HLA00293HLA02483_HLA00162HLA02489_HLA01741HLA02490_HLA00146HLA02490_HLA01717HLA02492_HLA00181HLA02496_HLA00146HLA02498_HLA00291HLA02499_HLA00225HLA02503_HLA00335HLA02504_HLA00267HLA02505_HLA00265HLA02506_HLA00244HLA02512_HLA00386HLA02513_HLA00223HLA02513_HLA00225HLA02514_HLA00132HLA02515_HLA00181HLA02516_HLA00153HLA02517_HLA00335HLA02518_HLA00368HLA02532_HLA00265HLA02536_HLA00292HLA02539_HLA02677HLA02545_HLA00162HLA02565_HLA00376HLA02566_HLA00237HLA02585_HLA00362HLA02588_HLA00291HLA02589_HLA00389HLA02591_HLA00146HLA02591_HLA01717HLA02596_HLA00386HLA02597_HLA00293HLA02618_HLA00162HLA02619_HLA00152HLA02620_HLA00344HLA02635_HLA00364HLA02636_HLA02352HLA02639_HLA00162HLA02642_HLA00181HLA02643_HLA00316HLA02644_HLA00318HLA02644_HLA08401HLA02645_HLA00241HLA02665_HLA00162HLA02667_HLA00344HLA02671_HLA00369HLA02672_HLA00344HLA02672_HLA02558HLA02672_HLA00364HLA02673_HLA00174HLA02674_HLA00165HLA02678_HLA00291HLA02679_HLA00367HLA02684_HLA00318HLA02684_HLA08401HLA02685_HLA00331HLA02687_HLA00265HLA02691_HLA00379HLA02693_HLA00297HLA02693_HLA01430HLA02694_HLA00237HLA02695_HLA00319HLA02698_HLA00213HLA02698_HLA07768HLA02698_HLA01532HLA02699_HLA00213HLA02699_HLA07768HLA02699_HLA01532HLA02700_HLA00318HLA02700_HLA08401HLA02712_HLA00386HLA02713_HLA00132HLA02714_HLA00268HLA02716_HLA00367HLA02727_HLA00337HLA02736_HLA00331HLA02751_HLA00367HLA02752_HLA00367HLA02754_HLA00344HLA02756_HLA00237HLA02757_HLA00376HLA02759_HLA00162HLA02762_HLA00146HLA02762_HLA01717HLA02763_HLA00241HLA02767_HLA00335HLA02770_HLA00318HLA02770_HLA08401HLA02770_HLA01341HLA02771_HLA00146HLA02772_HLA06273HLA02773_HLA00181HLA02781_HLA00162HLA02782_HLA00368HLA02783_HLA00213HLA02783_HLA07768HLA02784_HLA00225HLA02792_HLA00170HLA02793_HLA00362HLA02796_HLA00132HLA02799_HLA00293HLA02805_HLA01742HLA02806_HLA00267HLA02808_HLA00331HLA02809_HLA00153HLA02810_HLA00239HLA02823_HLA00166HLA02826_HLA00225HLA02844_HLA00132HLA02845_HLA00369HLA02847_HLA00239HLA02852_HLA00376HLA02853_HLA00146HLA02864_HLA00292HLA02866_HLA00291HLA02872_HLA00153HLA02873_HLA00132HLA02874_HLA00265HLA02875_HLA00162HLA02880_HLA00386HLA02882_HLA00162HLA02883_HLA00318HLA02883_HLA08401HLA02884_HLA00297HLA02884_HLA01430HLA02888_HLA00383HLA02905_HLA00205HLA02905_HLA00331HLA02906_HLA00291HLA02909_HLA00237HLA02910_HLA00132HLA02913_HLA02850HLA02922_HLA00312HLA02924_HLA00344HLA02925_HLA00369HLA02926_HLA00271HLA02929_HLA00153HLA02930_HLA00152HLA02931_HLA00225HLA02933_HLA00344HLA02941_HLA00319HLA02942_HLA02352HLA02944_HLA00367HLA02949_HLA00132HLA02952_HLA00337HLA02965_HLA00335HLA02966_HLA00381HLA02967_HLA00346HLA02968_HLA00132HLA02974_HLA00166HLA02976_HLA00166HLA02977_HLA00237HLA02989_HLA00293HLA02995_HLA00213HLA02995_HLA07768HLA02995_HLA01532HLA03001_HLA00318HLA03001_HLA08401HLA03003_HLA00237HLA03006_HLA00273HLA03009_HLA00362HLA03014_HLA00237HLA03019_HLA00173HLA03020_HLA00335HLA03047_HLA00181HLA03051_HLA00268HLA03078_HLA00244HLA03080_HLA00162HLA03084_HLA00238HLA03085_HLA00345HLA03086_HLA00331HLA03087_HLA00162HLA03088_HLA00132HLA03089_HLA00132HLA03091_HLA00146HLA03092_HLA00167HLA03093_HLA00162HLA03094_HLA00165HLA03098_HLA00368HLA03099_HLA00344HLA03103_HLA00162HLA03104_HLA00244HLA03105_HLA00345HLA03125_HLA00237HLA03126_HLA00238HLA03129_HLA00381HLA03133_HLA00319HLA03134_HLA00146HLA03137_HLA01742HLA03138_HLA00152HLA03147_HLA00381HLA03148_HLA00386HLA03149_HLA00239HLA03150_HLA00381HLA03153_HLA00291HLA03161_HLA00318HLA03161_HLA08401HLA03164_HLA00146HLA03169_HLA00239HLA03173_HLA00291HLA03176_HLA00225HLA03178_HLA00344HLA03179_HLA00132HLA03180_HLA00213HLA03180_HLA07768HLA03180_HLA01532HLA03186_HLA00364HLA03190_HLA00318HLA03190_HLA08401HLA03195_HLA00368HLA03197_HLA01741HLA03198_HLA00241HLA03200_HLA00223HLA03203_HLA00319HLA03205_HLA00291HLA03209_HLA00364HLA03210_HLA00238HLA03215_HLA00162HLA03217_HLA00162HLA03220_HLA00293HLA03222_HLA00297HLA03222_HLA01430HLA03228_HLA00369HLA03231_HLA00291HLA03237_HLA00132HLA03243_HLA00293HLA03244_HLA00162HLA03245_HLA00297HLA03245_HLA01430HLA03248_HLA00386HLA03249_HLA00331HLA03256_HLA00291HLA03257_HLA00369HLA03258_HLA01343HLA03259_HLA00319HLA03260_HLA00132HLA03261_HLA00398HLA03262_HLA00241HLA03263_HLA00213HLA03263_HLA07768HLA03263_HLA01532HLA03264_HLA00132HLA03265_HLA00146HLA03265_HLA01717HLA03266_HLA00376HLA03267_HLA00174HLA03269_HLA00165HLA03270_HLA00291HLA03271_HLA00331HLA03272_HLA00344HLA03273_HLA00345HLA03274_HLA00364HLA03275_HLA00271HLA03276_HLA00227HLA03277_HLA00344HLA03278_HLA00225HLA03279_HLA00345HLA03281_HLA00162HLA03282_HLA00344HLA03283_HLA00158HLA03283_HLA02166HLA03288_HLA00237HLA03289_HLA00386HLA03293_HLA00362HLA03294_HLA00132HLA03299_HLA00329HLA03300_HLA00241HLA03302_HLA00190HLA03311_HLA00293HLA03312_HLA00293HLA03313_HLA00344HLA03313_HLA02558HLA03313_HLA00364HLA03314_HLA00271HLA03315_HLA00152HLA03316_HLA00386HLA03317_HLA00362HLA03318_HLA00158HLA03319_HLA00162HLA03320_HLA00383HLA03321_HLA00237HLA03322_HLA00368HLA03323_HLA00228HLA03324_HLA00237HLA03334_HLA00174HLA03335_HLA00237HLA03336_HLA00237HLA03337_HLA00238HLA03338_HLA00271HLA03339_HLA00293HLA03341_HLA00271HLA03342_HLA00132HLA03344_HLA00291HLA03345_HLA00319HLA03348_HLA00174HLA03350_HLA00265HLA03354_HLA00362HLA03355_HLA00344HLA03356_HLA00367HLA03358_HLA00318HLA03358_HLA08401HLA03359_HLA00318HLA03359_HLA08401HLA03360_HLA00320HLA03361_HLA00331HLA03366_HLA00369HLA03367_HLA00389HLA03368_HLA00362HLA03369_HLA00386HLA03387_HLA00367HLA03392_HLA00293HLA03393_HLA00319HLA03403_HLA00297HLA03403_HLA01430HLA03412_HLA00318HLA03412_HLA08401HLA03413_HLA00132HLA03424_HLA00368HLA03441_HLA01118HLA03442_HLA00331HLA03449_HLA00146HLA03449_HLA01717HLA03450_HLA00146HLA03450_HLA01717HLA03456_HLA00344HLA03460_HLA00346HLA03462_HLA00213HLA03462_HLA07768HLA03462_HLA01532HLA03463_HLA00213HLA03463_HLA07768HLA03463_HLA01532HLA03464_HLA00340HLA03465_HLA00344HLA03468_HLA00344HLA03471_HLA02676HLA03473_HLA00271HLA03476_HLA00238HLA03479_HLA00152HLA03480_HLA00367HLA03481_HLA00146HLA03481_HLA01717HLA03503_HLA00369HLA03505_HLA00346HLA03506_HLA00381HLA03507_HLA00381HLA03509_HLA00344HLA03510_HLA00213HLA03510_HLA07768HLA03510_HLA01532HLA03512_HLA00205HLA03513_HLA00369HLA03514_HLA00132HLA03516_HLA00344HLA03536_HLA00319HLA03537_HLA00389HLA03551_HLA00223HLA03554_HLA00225HLA03584_HLA00293HLA03591_HLA00152HLA03595_HLA00364HLA03602_HLA00297HLA03602_HLA01430HLA03603_HLA00162HLA03605_HLA02560HLA03606_HLA00181HLA03607_HLA00239HLA03608_HLA00344HLA03609_HLA00364HLA03610_HLA00132HLA03611_HLA00132HLA03612_HLA00213HLA03612_HLA07768HLA03612_HLA01532HLA03613_HLA00331HLA03614_HLA00162HLA03614_HLA01743HLA03615_HLA00167HLA03616_HLA00225HLA03617_HLA00344HLA03620_HLA00166HLA03621_HLA00271HLA03622_HLA00132HLA03625_HLA00238HLA03627_HLA00318HLA03627_HLA08401HLA03628_HLA00297HLA03628_HLA01430HLA03633_HLA00293HLA03637_HLA00386HLA03639_HLA00158HLA03639_HLA02166HLA03644_HLA00241HLA03645_HLA00315HLA03646_HLA00162HLA03647_HLA00271HLA03648_HLA01752HLA03658_HLA00132HLA03659_HLA00225HLA03660_HLA00132HLA03661_HLA00225HLA03662_HLA00239HLA03663_HLA00146HLA03663_HLA01717HLA03664_HLA00158HLA03665_HLA00344HLA03666_HLA00381HLA03674_HLA00344HLA03675_HLA00381HLA03676_HLA00344HLA03677_HLA00225HLA03679_HLA00132HLA03692_HLA00132HLA03693_HLA00166HLA03694_HLA00267HLA03695_HLA00319HLA03708_HLA00162HLA03711_HLA00162HLA03712_HLA00225HLA03715_HLA00174HLA03716_HLA00344HLA03717_HLA00213HLA03717_HLA07768HLA03717_HLA01532HLA03718_HLA00318HLA03718_HLA08401HLA03719_HLA00344HLA03720_HLA00132HLA03722_HLA00239HLA03747_HLA02165HLA03756_HLA00280HLA03757_HLA00293HLA03761_HLA00132HLA03762_HLA00389HLA03770_HLA00152HLA03778_HLA00331HLA03780_HLA00291HLA03796_HLA00237HLA03797_HLA00344HLA03804_HLA00181HLA03810_HLA00225HLA03823_HLA00146HLA03823_HLA01717HLA03823_HLA02165HLA03824_HLA00225HLA03841_HLA00367HLA03900_HLA00132HLA03901_HLA00344HLA03902_HLA00146HLA03902_HLA01717HLA03903_HLA00318HLA03903_HLA08401HLA03904_HLA00381HLA03905_HLA00312HLA03906_HLA00188HLA03907_HLA00319HLA03908_HLA00265HLA03909_HLA00331HLA03933_HLA00137HLA03934_HLA00132HLA03935_HLA00146HLA03935_HLA01717HLA03936_HLA00137HLA03937_HLA00132HLA03938_HLA00132HLA03939_HLA00146HLA03939_HLA01717HLA03940_HLA00132HLA03941_HLA00146HLA03941_HLA01717HLA03942_HLA00132HLA03944_HLA00152HLA03945_HLA00315HLA03946_HLA00213HLA03946_HLA07768HLA03946_HLA01532HLA03947_HLA00162HLA03948_HLA00318HLA03948_HLA08401HLA03949_HLA00162HLA03950_HLA00318HLA03950_HLA08401HLA03951_HLA00180HLA03951_HLA01439HLA03952_HLA00225HLA03953_HLA00318HLA03953_HLA08401HLA03954_HLA00166HLA03955_HLA00225HLA03956_HLA00213HLA03956_HLA07768HLA03956_HLA01532HLA03957_HLA00213HLA03957_HLA07768HLA03957_HLA01532HLA03958_HLA00166HLA03959_HLA00265HLA03960_HLA00318HLA03960_HLA08401HLA03961_HLA00162HLA03962_HLA00318HLA03962_HLA08401HLA03963_HLA00237HLA03964_HLA00162HLA03965_HLA00312HLA03966_HLA00331HLA03967_HLA00369HLA03968_HLA00386HLA03969_HLA00381HLA03970_HLA00362HLA03971_HLA00344HLA03972_HLA00344HLA03973_HLA00318HLA03973_HLA08401HLA03974_HLA00318HLA03974_HLA08401HLA03981_HLA00132HLA03982_HLA00152HLA03983_HLA00369HLA03984_HLA00381HLA03985_HLA00180HLA03985_HLA01439HLA03986_HLA00381HLA03987_HLA00223HLA03990_HLA00162HLA04013_HLA00319HLA04014_HLA00319HLA04015_HLA00344HLA04017_HLA00369HLA04022_HLA00319HLA04023_HLA00181HLA04024_HLA00376HLA04025_HLA00386HLA04027_HLA00158HLA04027_HLA02166HLA04028_HLA00165HLA04041_HLA00271HLA04042_HLA00132HLA04043_HLA00271HLA04044_HLA00326HLA04045_HLA00344HLA04046_HLA00381HLA04047_HLA00368HLA04048_HLA00225HLA04049_HLA00341HLA04050_HLA00271HLA04051_HLA01343HLA04052_HLA00162HLA04053_HLA00225HLA04054_HLA00225HLA04055_HLA00158HLA04055_HLA00271HLA04056_HLA00319HLA04058_HLA00132HLA04059_HLA00344HLA04060_HLA00381HLA04066_HLA00158HLA04066_HLA02166HLA04067_HLA00132HLA04070_HLA00291HLA04071_HLA00162HLA04072_HLA00271HLA04073_HLA00265HLA04074_HLA02560HLA04075_HLA00213HLA04075_HLA07768HLA04075_HLA01532HLA04076_HLA00267HLA04077_HLA00376HLA04078_HLA00162HLA04079_HLA00132HLA04080_HLA00344HLA04081_HLA00146HLA04081_HLA01717HLA04082_HLA00319HLA04083_HLA00153HLA04084_HLA00162HLA04085_HLA00318HLA04085_HLA08401HLA04086_HLA00319HLA04087_HLA00386HLA04088_HLA00213HLA04088_HLA07768HLA04088_HLA01532HLA04089_HLA00225HLA04090_HLA00267HLA04091_HLA00213HLA04091_HLA07768HLA04091_HLA01532HLA04092_HLA00132HLA04093_HLA00181HLA04094_HLA00312HLA04095_HLA00364HLA04096_HLA00318HLA04096_HLA08401HLA04097_HLA00132HLA04098_HLA00340HLA04099_HLA00132HLA04100_HLA00341HLA04101_HLA00158HLA04102_HLA00344HLA04103_HLA00319HLA04104_HLA00344HLA04105_HLA00271HLA04106_HLA00213HLA04106_HLA07768HLA04106_HLA01532HLA04107_HLA00153HLA04108_HLA00341HLA04109_HLA00137HLA04111_HLA00318HLA04111_HLA08401HLA04112_HLA00162HLA04113_HLA00132HLA04114_HLA00237HLA04115_HLA00362HLA04116_HLA00318HLA04116_HLA08401HLA04128_HLA00340HLA04157_HLA00174HLA04158_HLA00162HLA04159_HLA00162HLA04160_HLA00265HLA04161_HLA00271HLA04162_HLA00362HLA04163_HLA00331HLA04164_HLA00225HLA04165_HLA00181HLA04166_HLA00344HLA04168_HLA00315HLA04169_HLA00162HLA04170_HLA00291HLA04171_HLA00162HLA04172_HLA00132HLA04173_HLA00318HLA04173_HLA08401HLA04174_HLA00293HLA04175_HLA00225HLA04176_HLA00158HLA04177_HLA00271HLA04178_HLA00244HLA04179_HLA00237HLA04180_HLA00341HLA04181_HLA00237HLA04182_HLA00341HLA04183_HLA00238HLA04184_HLA00265HLA04185_HLA00368HLA04186_HLA00146HLA04186_HLA01717HLA04187_HLA00166HLA04188_HLA00146HLA04188_HLA01717HLA04189_HLA00213HLA04189_HLA07768HLA04189_HLA01532HLA04190_HLA00162HLA04191_HLA00132HLA04192_HLA00158HLA04193_HLA00132HLA04194_HLA00319HLA04195_HLA00152HLA04196_HLA00318HLA04196_HLA08401HLA04197_HLA00225HLA04198_HLA00132HLA04199_HLA00344HLA04200_HLA00271HLA04201_HLA00165HLA04202_HLA00213HLA04202_HLA07768HLA04202_HLA01532HLA04203_HLA00381HLA04204_HLA00344HLA04205_HLA00213HLA04205_HLA07768HLA04205_HLA01532HLA04206_HLA00344HLA04207_HLA00153HLA04208_HLA00265HLA04209_HLA00376HLA04210_HLA00146HLA04210_HLA01717HLA04211_HLA00368HLA04212_HLA00213HLA04212_HLA07768HLA04212_HLA01532HLA04213_HLA00162HLA04214_HLA00368HLA04215_HLA00318HLA04215_HLA08401HLA04216_HLA00162HLA04217_HLA00267HLA04218_HLA00162HLA04219_HLA00132HLA04220_HLA00293HLA04221_HLA00146HLA04221_HLA01717HLA04222_HLA00213HLA04222_HLA07768HLA04222_HLA01532HLA04223_HLA00213HLA04223_HLA07768HLA04223_HLA01532HLA04224_HLA00318HLA04224_HLA08401HLA04225_HLA02558HLA04226_HLA00386HLA04227_HLA00315HLA04228_HLA00318HLA04228_HLA08401HLA04229_HLA00265HLA04230_HLA00146HLA04230_HLA01717HLA04231_HLA00344HLA04232_HLA00181HLA04233_HLA00132HLA04234_HLA00146HLA04234_HLA01717HLA04235_HLA00344HLA04236_HLA00312HLA04237_HLA00237HLA04238_HLA00132HLA04239_HLA00341HLA04240_HLA00146HLA04240_HLA01717HLA04241_HLA00132HLA04242_HLA00180HLA04242_HLA01439HLA04243_HLA00137HLA04244_HLA00364HLA04245_HLA00335HLA04246_HLA00132HLA04247_HLA00312HLA04248_HLA00132HLA04249_HLA00213HLA04249_HLA07768HLA04249_HLA01532HLA04250_HLA00132HLA04251_HLA00344HLA04252_HLA00319HLA04387_HLA00293HLA04397_HLA00386HLA04401_HLA00383HLA04412_HLA00364HLA04413_HLA00162HLA04414_HLA00153HLA04415_HLA00158HLA04432_HLA00213HLA04432_HLA07768HLA04432_HLA01532HLA04433_HLA00335HLA04434_HLA00237HLA04435_HLA00383HLA04436_HLA00153HLA04437_HLA00239HLA04438_HLA00146HLA04438_HLA01717HLA04439_HLA00267HLA04440_HLA00278HLA04441_HLA00344HLA04442_HLA00146HLA04442_HLA01717HLA04443_HLA00225HLA04444_HLA00344HLA04445_HLA00213HLA04445_HLA07768HLA04445_HLA01532HLA04446_HLA00237HLA04447_HLA01188HLA04448_HLA00173HLA04449_HLA00223HLA04450_HLA00362HLA04451_HLA00278HLA04452_HLA00381HLA04453_HLA00213HLA04453_HLA07768HLA04453_HLA01532HLA04454_HLA00162HLA04455_HLA00318HLA04455_HLA08401HLA04456_HLA00381HLA04457_HLA00162HLA04458_HLA00162HLA04459_HLA00362HLA04460_HLA00326HLA04461_HLA00166HLA04461_HLA02165HLA04462_HLA00364HLA04463_HLA00162HLA04464_HLA00162HLA04468_HLA00237HLA04471_HLA00165HLA04472_HLA00278HLA04473_HLA00165HLA04474_HLA00237HLA04475_HLA00267HLA04481_HLA00329HLA04495_HLA00344HLA04496_HLA00158HLA04497_HLA00237HLA04498_HLA00362HLA04499_HLA00146HLA04499_HLA01717HLA04500_HLA00181HLA04501_HLA00318HLA04501_HLA08401HLA04502_HLA00153HLA04503_HLA00331HLA04504_HLA00146HLA04504_HLA01717HLA04505_HLA00344HLA04506_HLA00386HLA04507_HLA00146HLA04507_HLA01717HLA04508_HLA00162HLA04509_HLA00225HLA04510_HLA00213HLA04510_HLA07768HLA04510_HLA01532HLA04511_HLA00265HLA04512_HLA00369HLA04513_HLA00344HLA04514_HLA00319HLA04515_HLA00146HLA04515_HLA01717HLA04516_HLA00146HLA04516_HLA01717HLA04517_HLA00364HLA04518_HLA00344HLA04519_HLA00318HLA04519_HLA08401HLA04520_HLA00146HLA04520_HLA01717HLA04521_HLA00237HLA04526_HLA00319HLA04532_HLA00158HLA04533_HLA00162HLA04534_HLA00318HLA04534_HLA08401HLA04535_HLA00340HLA04536_HLA00318HLA04536_HLA08401HLA04537_HLA00344HLA04538_HLA00340HLA04539_HLA00265HLA04540_HLA00319HLA04541_HLA00318HLA04541_HLA08401HLA04542_HLA00319HLA04543_HLA00293HLA04544_HLA00237HLA04551_HLA00344HLA04552_HLA00376HLA04553_HLA00162HLA04554_HLA00153HLA04555_HLA00376HLA04556_HLA00318HLA04556_HLA08401HLA04563_HLA00318HLA04563_HLA08401HLA04564_HLA00225HLA04565_HLA00158HLA04566_HLA00213HLA04566_HLA07768HLA04566_HLA01532HLA04567_HLA00153HLA04568_HLA00318HLA04568_HLA08401HLA04569_HLA00162HLA04571_HLA00132HLA04573_HLA02676HLA04580_HLA00152HLA04582_HLA00238HLA04635_HLA02376HLA04641_HLA00386HLA04648_HLA00293HLA04649_HLA00344HLA04650_HLA00152HLA04675_HLA00237HLA04684_HLA00162HLA04692_HLA00265HLA04703_HLA00381HLA04704_HLA00344HLA04705_HLA00344HLA04706_HLA00340HLA04707_HLA00344HLA04708_HLA00146HLA04708_HLA01717HLA04709_HLA00332HLA04709_HLA01437HLA04711_HLA00344HLA04712_HLA00393HLA04713_HLA00364HLA04714_HLA00318HLA04714_HLA08401HLA04715_HLA00223HLA04716_HLA00345HLA04718_HLA00344HLA04719_HLA00367HLA04720_HLA00146HLA04720_HLA01717HLA04722_HLA00146HLA04722_HLA01717HLA04727_HLA01118HLA04728_HLA00291HLA04729_HLA00345HLA04730_HLA00271HLA04732_HLA00367HLA04733_HLA00362HLA04734_HLA00331HLA04735_HLA00367HLA04738_HLA00265HLA04742_HLA00174HLA04743_HLA00331HLA04750_HLA00335HLA04752_HLA00213HLA04752_HLA07768HLA04752_HLA01532HLA04753_HLA00146HLA04753_HLA01717HLA04754_HLA00319HLA04755_HLA00381HLA04768_HLA00376HLA04769_HLA00225HLA04770_HLA00162HLA04771_HLA00225HLA04781_HLA00137HLA04787_HLA00153HLA04788_HLA00146HLA04788_HLA01717HLA04789_HLA00239HLA04790_HLA00332HLA04790_HLA01437HLA04791_HLA00344HLA04792_HLA00174HLA04796_HLA00280HLA04805_HLA00213HLA04805_HLA07768HLA04805_HLA01532HLA04806_HLA00376HLA04815_HLA00319HLA04816_HLA00146HLA04816_HLA01717HLA04817_HLA00364HLA04818_HLA00293HLA04819_HLA00376HLA04820_HLA00241HLA04821_HLA00368HLA04846_HLA00291HLA04847_HLA00319HLA04848_HLA00381HLA04849_HLA00153HLA04860_HLA00146HLA04860_HLA01717HLA04861_HLA00378HLA04864_HLA00174HLA04866_HLA00174HLA04867_HLA00237HLA04868_HLA00291HLA04872_HLA00237HLA04873_HLA00291HLA04875_HLA00297HLA04875_HLA01430HLA04877_HLA00291HLA04878_HLA01510HLA04879_HLA00174HLA04880_HLA00153HLA04880_HLA00297HLA04880_HLA01430HLA04881_HLA00291HLA04882_HLA00237HLA04884_HLA00137HLA04886_HLA00132HLA04888_HLA00239HLA04889_HLA00318HLA04889_HLA08401HLA04892_HLA00237HLA04900_HLA00244HLA04901_HLA00291HLA04902_HLA00291HLA04903_HLA00291HLA04904_HLA00237HLA04907_HLA00237HLA04910_HLA00237HLA04911_HLA00244HLA04912_HLA00297HLA04912_HLA01430HLA04913_HLA00239HLA04914_HLA00237HLA04915_HLA00293HLA04916_HLA00237HLA04917_HLA00293HLA04918_HLA00291HLA04919_HLA00239HLA04920_HLA00293HLA04921_HLA00237HLA04922_HLA00237HLA04923_HLA00237HLA04924_HLA00132HLA04925_HLA00132HLA04929_HLA00132HLA04930_HLA00297HLA04930_HLA01430HLA04931_HLA00132HLA04932_HLA00241HLA04933_HLA00137HLA04934_HLA00293HLA04935_HLA00132HLA04936_HLA00237HLA04937_HLA00291HLA04938_HLA00237HLA04939_HLA00291HLA04940_HLA00291HLA04941_HLA00174HLA04946_HLA00237HLA04947_HLA00293HLA04959_HLA00237HLA04960_HLA00237HLA04961_HLA00237HLA04962_HLA00237HLA04963_HLA00237HLA04964_HLA00132HLA04965_HLA00237HLA04966_HLA00132HLA04967_HLA00237HLA04977_HLA00291HLA04978_HLA00237HLA04979_HLA00291HLA04980_HLA00239HLA04981_HLA00132HLA04992_HLA00239HLA04993_HLA00132HLA04994_HLA00318HLA04994_HLA08401HLA04997_HLA00291HLA04998_HLA00238HLA04999_HLA00237HLA05000_HLA00132HLA05009_HLA00237HLA05010_HLA00293HLA05011_HLA00293HLA05018_HLA02850HLA05021_HLA00293HLA05047_HLA00237HLA05048_HLA00318HLA05048_HLA08401HLA05049_HLA00319HLA05050_HLA00297HLA05050_HLA01430HLA05051_HLA00237HLA05052_HLA00318HLA05052_HLA08401HLA05053_HLA00291HLA05054_HLA00293HLA05055_HLA00319HLA05056_HLA00237HLA05057_HLA00318HLA05057_HLA08401HLA05058_HLA00237HLA05059_HLA00244HLA05060_HLA00237HLA05061_HLA00237HLA05062_HLA00319HLA05063_HLA00237HLA05092_HLA00319HLA05093_HLA00291HLA05094_HLA00132HLA05095_HLA00137HLA05096_HLA00291HLA05097_HLA02850HLA05099_HLA00319HLA05106_HLA00132HLA05112_HLA00369HLA05125_HLA00213HLA05125_HLA07768HLA05125_HLA01532HLA05126_HLA00293HLA05127_HLA00146HLA05127_HLA01717HLA05134_HLA00152HLA05135_HLA00162HLA05151_HLA00292HLA05152_HLA00291HLA05153_HLA00291HLA05154_HLA00301HLA05222_HLA00132HLA05223_HLA00362HLA05253_HLA00132HLA05254_HLA00152HLA05256_HLA00153HLA05257_HLA00162HLA05258_HLA00162HLA05259_HLA00165HLA05260_HLA00190HLA05263_HLA00180HLA05263_HLA01439HLA05264_HLA00181HLA05266_HLA00162HLA05267_HLA00223HLA05270_HLA00237HLA05271_HLA00237HLA05272_HLA00237HLA05273_HLA00237HLA05274_HLA00174HLA05275_HLA00271HLA05277_HLA00292HLA05278_HLA00292HLA05279_HLA00292HLA05280_HLA00292HLA05281_HLA00292HLA05283_HLA00293HLA05284_HLA00293HLA05285_HLA00293HLA05287_HLA00331HLA05288_HLA00337HLA05289_HLA00344HLA05290_HLA00146HLA05292_HLA00271HLA05294_HLA00369HLA05295_HLA00369HLA05296_HLA00369HLA05297_HLA00386HLA05298_HLA00386HLA05301_HLA00268HLA05304_HLA00329HLA05305_HLA00293HLA05306_HLA00398HLA05308_HLA00315HLA05320_HLA00381HLA05362_HLA00146HLA05363_HLA00292HLA05369_HLA00181HLA05381_HLA00162HLA05386_HLA00392HLA05390_HLA00137HLA05391_HLA00291HLA05393_HLA00301HLA05400_HLA00225HLA05401_HLA00367HLA05404_HLA00225HLA05405_HLA00162HLA05406_HLA00319HLA05410_HLA00292HLA05424_HLA00383HLA05464_HLA00344HLA05465_HLA00381HLA05466_HLA00341HLA05467_HLA00291HLA05468_HLA00344HLA05469_HLA00344HLA05470_HLA00341HLA05471_HLA00162HLA05472_HLA00162HLA05473_HLA02370HLA05474_HLA00158HLA05474_HLA02166HLA05475_HLA00338HLA05476_HLA00381HLA05477_HLA00225HLA05478_HLA00368HLA05479_HLA00188HLA05480_HLA00331HLA05481_HLA00319HLA05482_HLA00146HLA05482_HLA01717HLA05483_HLA00213HLA05483_HLA07768HLA05483_HLA01532HLA05484_HLA00340HLA05485_HLA00213HLA05485_HLA07768HLA05485_HLA01532HLA05486_HLA00362HLA05487_HLA00265HLA05488_HLA00344HLA05489_HLA00162HLA05490_HLA00158HLA05490_HLA02166HLA05491_HLA00239HLA05492_HLA00225HLA05493_HLA00291HLA05494_HLA00344HLA05495_HLA00344HLA05496_HLA00340HLA05497_HLA00362HLA05498_HLA00340HLA05499_HLA00341HLA05500_HLA00162HLA05501_HLA00165HLA05502_HLA00376HLA05503_HLA00381HLA05504_HLA00225HLA05505_HLA00312HLA05506_HLA00146HLA05506_HLA01717HLA05507_HLA00368HLA05508_HLA00213HLA05508_HLA07768HLA05508_HLA01532HLA05509_HLA00170HLA05510_HLA00146HLA05510_HLA01717HLA05511_HLA00271HLA05512_HLA00132HLA05513_HLA00381HLA05514_HLA00271HLA05515_HLA00312HLA05516_HLA00180HLA05516_HLA01439HLA05517_HLA00225HLA05518_HLA00386HLA05519_HLA00267HLA05520_HLA00291HLA05525_HLA00268HLA05531_HLA00132HLA05533_HLA00312HLA05534_HLA00319HLA05535_HLA00239HLA05536_HLA00344HLA05537_HLA00297HLA05537_HLA01430HLA05538_HLA00312HLA05562_HLA00381HLA05563_HLA00381HLA05694_HLA00344HLA05695_HLA00291HLA05695_HLA00301HLA05712_HLA00267HLA05713_HLA00237HLA05714_HLA00280HLA05715_HLA00344HLA05716_HLA00137HLA05717_HLA00318HLA05717_HLA08401HLA05718_HLA00162HLA05719_HLA00265HLA05720_HLA00146HLA05720_HLA01717HLA05721_HLA00318HLA05721_HLA08401HLA05722_HLA00340HLA05723_HLA00344HLA05756_HLA00369HLA05802_HLA00369HLA05804_HLA00291HLA05806_HLA00344HLA05808_HLA00390HLA05809_HLA00153HLA05810_HLA00174HLA05811_HLA00292HLA05812_HLA00331HLA05813_HLA00331HLA05815_HLA00292HLA05816_HLA00292HLA05824_HLA00291HLA05826_HLA00237HLA05828_HLA00238HLA05829_HLA00318HLA05829_HLA08401HLA05830_HLA00239HLA05833_HLA00312HLA05834_HLA00340HLA05835_HLA00241HLA05836_HLA00344HLA05840_HLA00345HLA05841_HLA00239HLA05842_HLA00291HLA05843_HLA02584HLA05856_HLA00291HLA05858_HLA00319HLA05859_HLA00293HLA05860_HLA00320HLA05861_HLA00146HLA05861_HLA01717HLA05862_HLA00364HLA05866_HLA02850HLA05877_HLA00319HLA05878_HLA00158HLA05912_HLA00344HLA05924_HLA00291HLA05925_HLA00225HLA05926_HLA00318HLA05926_HLA08401HLA05927_HLA00362HLA05928_HLA00158HLA05953_HLA00166HLA05954_HLA00293HLA05955_HLA00239HLA05956_HLA00331HLA05957_HLA00162HLA05958_HLA00381HLA05959_HLA00344HLA05960_HLA00158HLA05960_HLA00391HLA05962_HLA00267HLA05983_HLA00239HLA05997_HLA00238HLA05998_HLA00344HLA05999_HLA00364HLA06000_HLA00318HLA06000_HLA08401HLA06023_HLA00344HLA06024_HLA00153HLA06025_HLA00297HLA06025_HLA01430HLA06026_HLA00362HLA06030_HLA00294HLA06031_HLA00165HLA06033_HLA00174HLA06041_HLA00132HLA06045_HLA00318HLA06045_HLA08401HLA06050_HLA00364HLA06053_HLA00379HLA06056_HLA00153HLA06057_HLA00239HLA06058_HLA00386HLA06059_HLA00312HLA06060_HLA00378HLA06060_HLA00379HLA06061_HLA00132HLA06130_HLA00166HLA06133_HLA00162HLA06134_HLA00239HLA06135_HLA00213HLA06135_HLA07768HLA06135_HLA01532HLA06148_HLA00239HLA06149_HLA00152HLA06152_HLA00318HLA06152_HLA08401HLA06155_HLA00293HLA06158_HLA00346HLA06160_HLA00367HLA06161_HLA00386HLA06182_HLA03651HLA06183_HLA00225HLA06184_HLA00180HLA06184_HLA01439HLA06185_HLA00213HLA06185_HLA07768HLA06185_HLA01532HLA06186_HLA00368HLA06187_HLA00132HLA06210_HLA00291HLA06211_HLA00340HLA06212_HLA00225HLA06213_HLA00213HLA06213_HLA07768HLA06213_HLA01532HLA06214_HLA00213HLA06214_HLA07768HLA06214_HLA01532HLA06215_HLA00146HLA06215_HLA01717HLA06216_HLA00318HLA06216_HLA08401HLA06217_HLA00318HLA06217_HLA08401HLA06218_HLA00319HLA06219_HLA00332HLA06219_HLA01437HLA06220_HLA00239HLA06221_HLA00362HLA06222_HLA00162HLA06223_HLA00315HLA06224_HLA00132HLA06225_HLA00137HLA06226_HLA00386HLA06227_HLA00340HLA06228_HLA00291HLA06229_HLA00383HLA06230_HLA00225HLA06231_HLA00265HLA06232_HLA00213HLA06232_HLA07768HLA06232_HLA01532HLA06233_HLA00213HLA06233_HLA07768HLA06233_HLA01532HLA06234_HLA00213HLA06234_HLA07768HLA06234_HLA01532HLA06235_HLA00153HLA06236_HLA00153HLA06237_HLA00318HLA06237_HLA08401HLA06238_HLA00341HLA06239_HLA00238HLA06240_HLA00381HLA06241_HLA00381HLA06242_HLA00267HLA06243_HLA00213HLA06243_HLA07768HLA06243_HLA01532HLA06244_HLA00319HLA06245_HLA00318HLA06245_HLA08401HLA06246_HLA00320HLA06247_HLA00319HLA06248_HLA00162HLA06249_HLA00383HLA06250_HLA00381HLA06251_HLA00344HLA06252_HLA00312HLA06253_HLA00291HLA06254_HLA00341HLA06255_HLA00225HLA06256_HLA00225HLA06257_HLA00265HLA06258_HLA00146HLA06258_HLA01717HLA06259_HLA00146HLA06259_HLA01717HLA06260_HLA00146HLA06260_HLA01717HLA06261_HLA00244HLA06262_HLA00320HLA06263_HLA00153HLA06264_HLA00153HLA06265_HLA00318HLA06265_HLA08401HLA06266_HLA00237HLA06267_HLA00162HLA06268_HLA00344HLA06269_HLA00346HLA06270_HLA00344HLA06271_HLA00284HLA06278_HLA00239HLA06280_HLA00291HLA06281_HLA00297HLA06281_HLA01430HLA06282_HLA00181HLA06284_HLA00367HLA06285_HLA00132HLA06286_HLA00315HLA06288_HLA00344HLA06289_HLA00318HLA06289_HLA08401HLA06292_HLA00223HLA06301_HLA00318HLA06301_HLA08401HLA06302_HLA00297HLA06302_HLA01430HLA06313_HLA00331HLA06314_HLA00293HLA06315_HLA00381HLA06316_HLA00267HLA06317_HLA00132HLA06318_HLA00132HLA06319_HLA00132HLA06320_HLA00271HLA06321_HLA00265HLA06322_HLA00213HLA06322_HLA07768HLA06322_HLA01532HLA06323_HLA00320HLA06324_HLA00158HLA06325_HLA00158HLA06326_HLA00268HLA06327_HLA00179HLA06352_HLA00340HLA06353_HLA00225HLA06354_HLA00213HLA06354_HLA07768HLA06354_HLA01532HLA06355_HLA00362HLA06356_HLA00344HLA06357_HLA00158HLA06358_HLA00213HLA06358_HLA07768HLA06358_HLA01532HLA06360_HLA00331HLA06364_HLA00344HLA06365_HLA00344HLA06366_HLA00179HLA06369_HLA00344HLA06374_HLA00152HLA06380_HLA00213HLA06380_HLA07768HLA06380_HLA01532HLA06519_HLA00369HLA06574_HLA00238HLA06575_HLA02851HLA06578_HLA02343HLA06579_HLA00344HLA06580_HLA00237HLA06581_HLA00213HLA06581_HLA07768HLA06581_HLA01532HLA06584_HLA00379HLA06585_HLA00267HLA06642_HLA00319HLA06645_HLA00319HLA06646_HLA00318HLA06646_HLA08401HLA06647_HLA00238HLA06648_HLA00239HLA06649_HLA00386HLA06650_HLA00378HLA06650_HLA00379HLA06651_HLA00237HLA06652_HLA00165HLA06653_HLA01510HLA06654_HLA00205HLA06660_HLA00213HLA06660_HLA07768HLA06660_HLA01532HLA06664_HLA00146HLA06664_HLA01717HLA06675_HLA00344HLA06676_HLA00344HLA06677_HLA00132HLA06678_HLA00132HLA06679_HLA00132HLA06680_HLA00162HLA06681_HLA00297HLA06681_HLA01430HLA06682_HLA00146HLA06682_HLA01717HLA06683_HLA00381HLA06684_HLA00244HLA06685_HLA00237HLA06686_HLA00237HLA06687_HLA00364HLA06688_HLA00383HLA06689_HLA00237HLA06690_HLA00132HLA06691_HLA00132HLA06692_HLA00267HLA06693_HLA00291HLA06694_HLA02850HLA06694_HLA00312HLA06695_HLA00291HLA06696_HLA00291HLA06697_HLA00312HLA06698_HLA00345HLA06699_HLA00153HLA06700_HLA00381HLA06701_HLA00344HLA06702_HLA00132HLA06703_HLA00132HLA06815_HLA00239HLA06816_HLA00344HLA06825_HLA00213HLA06825_HLA07768HLA06825_HLA01532HLA06826_HLA00132HLA06830_HLA00267HLA06831_HLA00179HLA06834_HLA00267HLA06835_HLA00341HLA06871_HLA00132HLA06883_HLA00381HLA06884_HLA00237HLA06885_HLA00181HLA06887_HLA00297HLA06887_HLA01430HLA06888_HLA00162HLA06889_HLA00331HLA06891_HLA00340HLA06905_HLA00132HLA06914_HLA00291HLA06915_HLA00293HLA06916_HLA00265HLA06917_HLA00146HLA06917_HLA01717HLA06918_HLA00146HLA06918_HLA01717HLA06919_HLA00162HLA06920_HLA00368HLA06921_HLA00173HLA06922_HLA00132HLA06923_HLA00132HLA06924_HLA00132HLA06925_HLA00340HLA06926_HLA00225HLA06927_HLA00213HLA06927_HLA07768HLA06927_HLA01532HLA06928_HLA00146HLA06928_HLA01717HLA06929_HLA00239HLA06930_HLA00180HLA06930_HLA01439HLA06931_HLA00284HLA06932_HLA00340HLA06933_HLA00153HLA06934_HLA00364HLA06935_HLA00237HLA06936_HLA00344HLA06937_HLA00393HLA06938_HLA00280HLA06939_HLA00291HLA06940_HLA00225HLA06941_HLA00265HLA06942_HLA00381HLA06943_HLA00146HLA06943_HLA01717HLA06944_HLA00318HLA06944_HLA08401HLA06945_HLA00237HLA06946_HLA00238HLA06947_HLA00162HLA06948_HLA00162HLA06949_HLA00381HLA06950_HLA00158HLA06951_HLA00271HLA06952_HLA00271HLA06953_HLA00271HLA06954_HLA00326HLA06955_HLA00225HLA06956_HLA00146HLA06956_HLA01717HLA06957_HLA00153HLA06958_HLA00153HLA06959_HLA00345HLA06960_HLA00237HLA06961_HLA00239HLA06962_HLA00244HLA06963_HLA00362HLA06964_HLA00237HLA06965_HLA00176HLA06966_HLA00162HLA06967_HLA00368HLA06968_HLA00376HLA06969_HLA00344HLA06970_HLA00132HLA06971_HLA00267HLA06972_HLA00291HLA06973_HLA00291HLA06974_HLA00381HLA06975_HLA00153HLA06976_HLA00318HLA06976_HLA08401HLA06977_HLA00244HLA06978_HLA00362HLA06979_HLA00344HLA06980_HLA00137HLA06981_HLA00132HLA06982_HLA00292HLA06983_HLA00293HLA06984_HLA00146HLA06984_HLA01717HLA06985_HLA00318HLA06985_HLA08401HLA06986_HLA00318HLA06986_HLA08401HLA06987_HLA00237HLA06988_HLA00162HLA06988_HLA01743HLA06989_HLA00381HLA06990_HLA00158HLA06990_HLA02166HLA06991_HLA00268HLA06992_HLA00179HLA06993_HLA00225HLA06994_HLA00265HLA06995_HLA00213HLA06995_HLA07768HLA06995_HLA01532HLA06996_HLA00146HLA06996_HLA01717HLA06997_HLA00162HLA06998_HLA00318HLA06998_HLA08401HLA06999_HLA00237HLA07000_HLA00362HLA07001_HLA00344HLA07002_HLA00344HLA07003_HLA00237HLA07004_HLA00158HLA07032_HLA00318HLA07032_HLA08401HLA07033_HLA00152HLA07035_HLA00137HLA07039_HLA00132HLA07087_HLA00318HLA07087_HLA08401HLA07090_HLA00319HLA07093_HLA00166HLA07094_HLA00152HLA07095_HLA00293HLA07103_HLA00362HLA07177_HLA00225HLA07178_HLA00238HLA07179_HLA00162HLA07180_HLA00344HLA07181_HLA00344HLA07186_HLA00341HLA07187_HLA00225HLA07188_HLA00225HLA07189_HLA00213HLA07189_HLA07768HLA07189_HLA01532HLA07190_HLA00158HLA07191_HLA00146HLA07191_HLA01717HLA07192_HLA00364HLA07193_HLA00318HLA07193_HLA08401HLA07194_HLA00318HLA07194_HLA08401HLA07195_HLA00241HLA07196_HLA00239HLA07197_HLA00237HLA07198_HLA00239HLA07199_HLA00386HLA07200_HLA00381HLA07201_HLA00368HLA07202_HLA00238HLA07203_HLA00344HLA07204_HLA00344HLA07205_HLA00137HLA07206_HLA00132HLA07207_HLA00132HLA07208_HLA00132HLA07209_HLA00335HLA07210_HLA00335HLA07211_HLA00267HLA07212_HLA00238HLA07280_HLA00331HLA07285_HLA00291HLA07302_HLA00238HLA07303_HLA00213HLA07303_HLA07768HLA07303_HLA01532HLA07304_HLA00297HLA07304_HLA01430HLA07305_HLA00132HLA07306_HLA00331HLA07307_HLA00271HLA07308_HLA00344HLA07309_HLA00386HLA07310_HLA00267HLA07314_HLA00368HLA07319_HLA00344HLA07325_HLA00331HLA07332_HLA00291HLA07335_HLA00244HLA07336_HLA00362HLA07339_HLA00223HLA07354_HLA00132HLA07384_HLA00293HLA07385_HLA00162HLA07388_HLA00318HLA07388_HLA08401HLA07412_HLA00181HLA07418_HLA00146HLA07418_HLA01717HLA07439_HLA00291HLA07440_HLA00293HLA07441_HLA00225HLA07442_HLA00146HLA07442_HLA01717HLA07443_HLA00146HLA07443_HLA01717HLA07444_HLA00146HLA07444_HLA01717HLA07445_HLA00146HLA07445_HLA01717HLA07446_HLA00146HLA07446_HLA01717HLA07447_HLA00318HLA07447_HLA08401HLA07448_HLA00319HLA07449_HLA00318HLA07449_HLA08401HLA07450_HLA00318HLA07450_HLA08401HLA07451_HLA00320HLA07452_HLA00244HLA07453_HLA00162HLA07454_HLA00237HLA07455_HLA00381HLA07456_HLA00381HLA07457_HLA00162HLA07458_HLA00162HLA07459_HLA00368HLA07460_HLA00376HLA07461_HLA00344HLA07462_HLA00344HLA07463_HLA00158HLA07464_HLA00132HLA07465_HLA00132HLA07466_HLA00132HLA07467_HLA00132HLA07468_HLA00132HLA07469_HLA00132HLA07470_HLA00267HLA07471_HLA00267HLA07472_HLA00271HLA07525_HLA00162HLA07535_HLA00367HLA07549_HLA00237HLA07552_HLA00265HLA07553_HLA00345HLA07560_HLA00237HLA07623_HLA00344HLA07624_HLA00312HLA07625_HLA00291HLA07626_HLA00291HLA07627_HLA00341HLA07628_HLA00293HLA07629_HLA00293HLA07630_HLA00297HLA07630_HLA01430HLA07631_HLA00225HLA07632_HLA00213HLA07632_HLA07768HLA07632_HLA01532HLA07633_HLA00213HLA07633_HLA07768HLA07633_HLA01532HLA07634_HLA00225HLA07635_HLA00146HLA07635_HLA01717HLA07636_HLA00146HLA07636_HLA01717HLA07637_HLA00146HLA07637_HLA01717HLA07638_HLA00146HLA07638_HLA01717HLA07639_HLA00318HLA07639_HLA08401HLA07640_HLA00319HLA07641_HLA00318HLA07641_HLA08401HLA07642_HLA00318HLA07642_HLA08401HLA07643_HLA00364HLA07644_HLA00237HLA07645_HLA00237HLA07646_HLA00237HLA07647_HLA00386HLA07648_HLA00386HLA07649_HLA00188HLA07650_HLA00162HLA07651_HLA00244HLA07652_HLA00166HLA07653_HLA00166HLA07654_HLA00344HLA07655_HLA00344HLA07656_HLA00344HLA07657_HLA00368HLA07658_HLA00158HLA07659_HLA00132HLA07660_HLA00132HLA07661_HLA00132HLA07662_HLA00132HLA07663_HLA00271HLA07664_HLA00271HLA07665_HLA00271HLA07679_HLA00213HLA07679_HLA07768HLA07679_HLA01532HLA07680_HLA00291HLA07681_HLA00292HLA07682_HLA00291HLA07683_HLA00329HLA07684_HLA00291HLA07685_HLA00293HLA07686_HLA00297HLA07686_HLA01430HLA07687_HLA00293HLA07688_HLA00293HLA07689_HLA00225HLA07690_HLA00265HLA07691_HLA00213HLA07691_HLA07768HLA07691_HLA01532HLA07692_HLA00239HLA07693_HLA00153HLA07694_HLA00153HLA07695_HLA00319HLA07696_HLA00319HLA07697_HLA00319HLA07698_HLA00318HLA07698_HLA08401HLA07699_HLA00320HLA07700_HLA00318HLA07700_HLA08401HLA07701_HLA00237HLA07702_HLA00364HLA07703_HLA00239HLA07704_HLA00237HLA07705_HLA00239HLA07706_HLA00237HLA07707_HLA00362HLA07708_HLA00381HLA07709_HLA00162HLA07710_HLA00368HLA07711_HLA00376HLA07712_HLA00166HLA07713_HLA00162HLA07714_HLA00344HLA07715_HLA00344HLA07716_HLA00344HLA07717_HLA00158HLA07718_HLA00267HLA07719_HLA00237HLA07720_HLA00267HLA07721_HLA00132HLA07722_HLA00132HLA07723_HLA00132HLA07724_HLA00132HLA07725_HLA00158HLA07725_HLA02166HLA07726_HLA00271HLA07727_HLA00267HLA07728_HLA00291HLA07748_HLA00383HLA07754_HLA00291HLA07758_HLA00367HLA07762_HLA00291HLA07764_HLA00376HLA07769_HLA00239HLA07780_HLA00241HLA07781_HLA00284HLA07792_HLA00241HLA07796_HLA00237HLA07800_HLA00362HLA07801_HLA00381HLA07808_HLA00318HLA07808_HLA08401HLA07809_HLA00213HLA07809_HLA07768HLA07809_HLA01532HLA07812_HLA00318HLA07812_HLA08401HLA07823_HLA00362HLA07890_HLA00291HLA07891_HLA00291HLA07892_HLA00153HLA07893_HLA00291HLA07894_HLA00291HLA07895_HLA00291HLA07896_HLA00291HLA07897_HLA00293HLA07898_HLA00293HLA07899_HLA00293HLA07900_HLA00293HLA07901_HLA00225HLA07902_HLA00225HLA07903_HLA00227HLA07904_HLA00213HLA07904_HLA07768HLA07904_HLA01532HLA07905_HLA00213HLA07905_HLA07768HLA07905_HLA01532HLA07906_HLA00213HLA07906_HLA07768HLA07906_HLA01532HLA07907_HLA00213HLA07907_HLA07768HLA07907_HLA01532HLA07908_HLA00213HLA07908_HLA07768HLA07908_HLA01532HLA07909_HLA00213HLA07909_HLA07768HLA07909_HLA01532HLA07910_HLA00213HLA07910_HLA07768HLA07910_HLA01532HLA07911_HLA00146HLA07911_HLA01717HLA07912_HLA00146HLA07912_HLA01717HLA07913_HLA00146HLA07913_HLA01717HLA07914_HLA00238HLA07915_HLA00153HLA07916_HLA00152HLA07917_HLA00153HLA07918_HLA00162HLA07919_HLA00291HLA07920_HLA00293HLA07921_HLA00293HLA07927_HLA00237HLA07928_HLA00162HLA07931_HLA00265HLA07932_HLA00225HLA07939_HLA00237HLA07958_HLA00340HLA07959_HLA00316HLA07960_HLA00345HLA07961_HLA00331HLA07962_HLA00291HLA07963_HLA00367HLA07964_HLA00344HLA07966_HLA00367HLA07968_HLA00341HLA08041_HLA00146HLA08041_HLA01717HLA08050_HLA00132HLA08058_HLA00153HLA08059_HLA00376HLA08060_HLA00320HLA08061_HLA00319HLA08062_HLA00239HLA08063_HLA00239HLA08064_HLA00362HLA08065_HLA00362HLA08066_HLA00364HLA08067_HLA00386HLA08068_HLA00162HLA08069_HLA00162HLA08070_HLA00188HLA08071_HLA00162HLA08072_HLA00162HLA08073_HLA00381HLA08074_HLA00173HLA08075_HLA00166HLA08076_HLA00344HLA08077_HLA00344HLA08078_HLA00344HLA08089_HLA00319HLA08097_HLA00146HLA08101_HLA00291HLA08102_HLA00293HLA08105_HLA00291HLA08106_HLA00293HLA08107_HLA00344HLA08108_HLA00244HLA08112_HLA00291HLA08122_HLA00340HLA08125_HLA00318HLA08125_HLA08401HLA08130_HLA00344HLA08131_HLA00319HLA08132_HLA00318HLA08132_HLA08401HLA08134_HLA00132HLA08135_HLA00132HLA08136_HLA00132HLA08137_HLA00132HLA08138_HLA00132HLA08139_HLA00271HLA08140_HLA00271HLA08141_HLA00146HLA08141_HLA01717HLA08142_HLA00271HLA08143_HLA00335HLA08144_HLA00179HLA08247_HLA00331HLA08283_HLA00271HLA08287_HLA00293HLA08290_HLA00312HLA08294_HLA00381HLA08296_HLA00291HLA08297_HLA00369HLA08301_HLA00291HLA08302_HLA00291HLA08305_HLA00132HLA08311_HLA00158HLA08314_HLA00331HLA08315_HLA00291HLA08316_HLA00237HLA08317_HLA00237HLA08319_HLA00237HLA08321_HLA00166HLA08321_HLA00378HLA08322_HLA00271HLA08323_HLA00291HLA08324_HLA00340HLA08325_HLA00291HLA08326_HLA00291HLA08327_HLA00225HLA08328_HLA00293HLA08329_HLA00228HLA08330_HLA00225HLA08331_HLA00225HLA08332_HLA00225HLA08333_HLA00265HLA08334_HLA00265HLA08335_HLA00213HLA08335_HLA07768HLA08335_HLA01532HLA08336_HLA00213HLA08336_HLA07768HLA08336_HLA01532HLA08337_HLA00265HLA08338_HLA00146HLA08338_HLA01717HLA08339_HLA00146HLA08339_HLA01717HLA08340_HLA00146HLA08340_HLA01717HLA08341_HLA00146HLA08341_HLA01717HLA08342_HLA00319HLA08343_HLA00146HLA08343_HLA01717HLA08344_HLA00237HLA08345_HLA00153HLA08346_HLA00153HLA08347_HLA00153HLA08348_HLA00319HLA08349_HLA00318HLA08349_HLA08401HLA08350_HLA00319HLA08351_HLA00319HLA08352_HLA00319HLA08353_HLA01510HLA08354_HLA00237HLA08355_HLA00364HLA08356_HLA00238HLA08357_HLA00237HLA08358_HLA00237HLA08359_HLA01741HLA08360_HLA00237HLA08361_HLA00237HLA08362_HLA00237HLA08363_HLA00362HLA08364_HLA00362HLA08365_HLA00386HLA08366_HLA00362HLA08367_HLA00386HLA08368_HLA00162HLA08369_HLA00162HLA08370_HLA00381HLA08371_HLA00381HLA08372_HLA00181HLA08373_HLA00181HLA08374_HLA00344HLA08375_HLA00344HLA08375_HLA02558HLA08375_HLA00364HLA08376_HLA00158HLA08377_HLA00344HLA08378_HLA00237HLA08379_HLA00132HLA08380_HLA00132HLA08381_HLA00132HLA08382_HLA00132HLA08383_HLA00132HLA08384_HLA00132HLA08385_HLA00132HLA08386_HLA00132HLA08387_HLA00398HLA08388_HLA00271HLA08389_HLA02584HLA08390_HLA00267HLA08391_HLA00344HLA08392_HLA00213HLA08392_HLA07768HLA08392_HLA01532HLA08393_HLA00237HLA08394_HLA00315HLA08396_HLA00293HLA08397_HLA00237HLA08398_HLA00331HLA08403_HLA00213HLA08403_HLA07768HLA08403_HLA01532HLA08405_HLA00162HLA08406_HLA00386HLA08409_HLA00162HLA08417_HLA00166HLA08432_HLA00319HLA08434_HLA00362HLA08435_HLA00237HLA08436_HLA00346HLA08439_HLA00291HLA08469_HLA00271HLA08470_HLA00132HLA08471_HLA00320HLA08472_HLA00225HLA08499_HLA00237HLA08500_HLA00291HLA08501_HLA00291HLA08502_HLA00312HLA08503_HLA00293HLA08504_HLA00225HLA08505_HLA00225HLA08506_HLA00213HLA08506_HLA07768HLA08506_HLA01532HLA08507_HLA00237HLA08508_HLA00146HLA08508_HLA01717HLA08509_HLA00146HLA08509_HLA01717HLA08510_HLA00146HLA08510_HLA01717HLA08511_HLA00319HLA08512_HLA00244HLA08513_HLA00237HLA08514_HLA00162HLA08515_HLA00162HLA08516_HLA00376HLA08517_HLA00318HLA08517_HLA08401HLA08518_HLA00376HLA08519_HLA00318HLA08519_HLA08401HLA08520_HLA00132HLA08521_HLA00132HLA08522_HLA00132HLA08523_HLA00132HLA08524_HLA00271HLA08525_HLA00344HLA08559_HLA00341HLA08563_HLA00331HLA08567_HLA00132HLA08568_HLA00345HLA08572_HLA00268HLA08573_HLA00152HLA08575_HLA00344HLA08576_HLA00367HLA08577_HLA00291HLA08578_HLA00162HLA08579_HLA00291HLA08581_HLA00146HLA08587_HLA00331HLA08594_HLA00297HLA08594_HLA01430HLA08597_HLA00271HLA08606_HLA00340HLA08653_HLA00344HLA08654_HLA00312HLA08655_HLA00312HLA08656_HLA00341HLA08657_HLA00312HLA08658_HLA00293HLA08659_HLA00293HLA08660_HLA00293HLA08661_HLA00225HLA08662_HLA00225HLA08663_HLA00213HLA08663_HLA07768HLA08663_HLA01532HLA08664_HLA00213HLA08664_HLA07768HLA08664_HLA01532HLA08665_HLA00146HLA08665_HLA01717HLA08666_HLA00146HLA08666_HLA01717HLA08667_HLA00146HLA08667_HLA01717HLA08668_HLA00146HLA08668_HLA01717HLA08669_HLA00146HLA08669_HLA01717HLA08670_HLA00340HLA08671_HLA02389HLA08672_HLA00318HLA08672_HLA08401HLA08673_HLA00318HLA08673_HLA08401HLA08674_HLA00321HLA08675_HLA00362HLA08676_HLA00237HLA08677_HLA00239HLA08678_HLA00162HLA08679_HLA00368HLA08680_HLA00344HLA08681_HLA00346HLA08682_HLA00344HLA08683_HLA00319HLA08684_HLA00137HLA08685_HLA00132HLA08686_HLA00132HLA08687_HLA00319HLA08779_HLA00265HLA08780_HLA02558HLA08780_HLA00364HLA08782_HLA00244HLA08783_HLA00162HLA08784_HLA00146HLA08784_HLA01717HLA08785_HLA00237HLA08790_HLA00152HLA08809_HLA00318HLA08809_HLA08401HLA08879_HLA00291HLA08880_HLA00344HLA08884_HLA00291HLA08894_HLA00341HLA08901_HLA00335HLA08902_HLA00152HLA08903_HLA00335HLA08907_HLA00166HLA08910_HLA00344HLA08911_HLA00223HLA08926_HLA00165HLA08927_HLA00381HLA08931_HLA00297HLA08931_HLA01430HLA08934_HLA00132HLA08936_HLA00213HLA08936_HLA07768HLA08936_HLA01532HLA08937_HLA00319HLA08962_HLA00368HLA08975_HLA00312HLA08976_HLA00291HLA08977_HLA00341HLA08978_HLA00293HLA08979_HLA00225HLA08980_HLA00225HLA08981_HLA00316HLA08982_HLA00213HLA08982_HLA07768HLA08982_HLA01532HLA08983_HLA00146HLA08983_HLA01717HLA08984_HLA00318HLA08984_HLA08401HLA08985_HLA00318HLA08985_HLA08401HLA08986_HLA00318HLA08986_HLA08401HLA08987_HLA00318HLA08987_HLA08401HLA08988_HLA00318HLA08988_HLA08401HLA08989_HLA00362HLA08990_HLA00239HLA08991_HLA00237HLA08992_HLA00237HLA08993_HLA00239HLA08994_HLA00237HLA08995_HLA00386HLA08996_HLA02676HLA08997_HLA00381HLA08998_HLA00376HLA08999_HLA00376HLA09000_HLA00166HLA09001_HLA00344HLA09002_HLA00344HLA09003_HLA00244HLA09004_HLA00158HLA09005_HLA00132HLA09006_HLA00132HLA09007_HLA00132HLA09008_HLA02560HLA09009_HLA00132HLA09010_HLA00271HLA09011_HLA00271HLA09074_HLA00162HLA09077_HLA00213HLA09077_HLA07768HLA09077_HLA01532HLA09084_HLA00364HLA09087_HLA00335HLA09098_HLA00237HLA09101_HLA00291HLA09112_HLA00146HLA09112_HLA01717HLA09116_HLA00137HLA09120_HLA00162HLA09131_HLA00268HLA09138_HLA00367HLA09153_HLA00297HLA09153_HLA01430HLA09154_HLA00344HLA09155_HLA00153HLA09167_HLA00340HLA09169_HLA00318HLA09169_HLA08401HLA09172_HLA00132HLA09173_HLA00271HLA09174_HLA00158HLA09174_HLA02166HLA09175_HLA00162HLA09302_HLA00386HLA09303_HLA00383HLA09305_HLA00319HLA09307_HLA00162HLA09308_HLA00225HLA09309_HLA00227HLA09310_HLA00312HLA09312_HLA00381HLA09313_HLA00315HLA09314_HLA00315HLA09315_HLA00386HLA09316_HLA00341HLA09317_HLA00344HLA09318_HLA00132HLA09326_HLA00223HLA09328_HLA00386HLA09338_HLA00132HLA09341_HLA00158HLA09345_HLA00213HLA09345_HLA07768HLA09345_HLA01532HLA09423_HLA00291HLA09424_HLA00312HLA09425_HLA00291HLA09426_HLA00225HLA09427_HLA00213HLA09427_HLA07768HLA09427_HLA01532HLA09428_HLA00213HLA09428_HLA07768HLA09428_HLA01532HLA09429_HLA00146HLA09429_HLA01717HLA09430_HLA00132HLA09431_HLA00153HLA09432_HLA00319HLA09433_HLA00318HLA09433_HLA08401HLA09434_HLA00318HLA09434_HLA08401HLA09435_HLA00237HLA09436_HLA00244HLA09437_HLA00162HLA09438_HLA00180HLA09438_HLA01439HLA09439_HLA00364HLA09440_HLA00166HLA09441_HLA00344HLA09442_HLA00153HLA09443_HLA00132HLA09444_HLA00132HLA09445_HLA00132HLA09446_HLA00132HLA09450_HLA00146HLA09452_HLA00223HLA09454_HLA00181HLA09456_HLA00153HLA09456_HLA00205HLA09461_HLA02850HLA09475_HLA00291HLA09482_HLA00389HLA09483_HLA00291HLA09487_HLA00132HLA09489_HLA00344HLA09491_HLA00132HLA09493_HLA00132HLA09500_HLA00367HLA09501_HLA00153HLA09504_HLA00239HLA09505_HLA00335HLA09513_HLA00213HLA09513_HLA07768HLA09513_HLA01532HLA09517_HLA00162HLA09554_HLA00312HLA09555_HLA00291HLA09556_HLA00213HLA09556_HLA07768HLA09556_HLA01532HLA09557_HLA00146HLA09557_HLA01717HLA09558_HLA00146HLA09558_HLA01717HLA09559_HLA00318HLA09559_HLA08401HLA09570_HLA00280HLA09571_HLA00237HLA09572_HLA00386HLA09573_HLA00162HLA09574_HLA00162HLA09575_HLA00162HLA09576_HLA00162HLA09577_HLA00381HLA09578_HLA00162HLA09579_HLA00376HLA09580_HLA00368HLA09581_HLA00368HLA09582_HLA00344HLA09583_HLA00331HLA09584_HLA00344HLA09585_HLA00158HLA09586_HLA00158HLA09587_HLA00158HLA09588_HLA00132HLA09589_HLA00132HLA09590_HLA00132HLA09591_HLA00132HLA09592_HLA00132HLA09593_HLA00280HLA09594_HLA00318HLA09594_HLA08401HLA09595_HLA00319HLA09645_HLA00153HLA09664_HLA00386HLA09681_HLA02352HLA09684_HLA00386HLA09695_HLA00166HLA09696_HLA00318HLA09696_HLA08401HLA09697_HLA00238HLA09698_HLA00386HLA09699_HLA00158HLA09699_HLA02163HLA09700_HLA00297HLA09700_HLA01430HLA09701_HLA01742HLA09702_HLA00291HLA09703_HLA00227HLA09704_HLA00293HLA09706_HLA00319HLA09708_HLA00166HLA09709_HLA00241HLA09710_HLA00376HLA09711_HLA00320HLA09722_HLA00376HLA09723_HLA00381HLA09724_HLA00132HLA09818_HLA00341HLA09821_HLA00331HLA09874_HLA00146HLA09874_HLA01717HLA09879_HLA00367HLA00401HLA00402HLA01555HLA01636HLA02790HLA03303HLA04020HLA05418HLA00405HLA02120HLA02170HLA03589HLA00410HLA05731HLA00411HLA00413HLA00414HLA02356HLA00415HLA00416HLA01412HLA02881HLA02987HLA03835HLA00420HLA01328HLA03572HLA08080HLA00423HLA00426HLA08413HLA05414HLA05543HLA00427HLA03586HLA01843HLA01856HLA00430HLA02561HLA03754HLA05526HLA00433HLA07937HLA08054HLA00434HLA01326HLA01902HLA07777HLA07778HLA03759HLA03976HLA00436HLA01554HLA00438HLA05419HLA01720HLA01889HLA02139HLA02354HLA02943HLA03753HLA03623HLA00445HLA00446HLA00447HLA00448HLA03626HLA03975HLA05416HLA05790HLA07938HLA00454HLA00455HLA02766HLA01413HLA01954HLA02605HLA03760HLA00462HLA00464HLA05415HLA00467HLA00471HLA02404HLA02438HLA00475HLA00476HLA00478HLA00481HLA00483HLA00404_HLA00405HLA00406_HLA00405HLA00408_HLA03589HLA00412_HLA00411HLA00417_HLA00413HLA00418_HLA00413HLA00419_HLA00413HLA00421_HLA00420HLA00421_HLA01328HLA00421_HLA03572HLA00421_HLA08080HLA00424_HLA00420HLA00424_HLA01328HLA00424_HLA03572HLA00424_HLA08080HLA00425_HLA00420HLA00425_HLA01328HLA00425_HLA03572HLA00425_HLA08080HLA00431_HLA00430HLA00431_HLA02561HLA00431_HLA05526HLA00432_HLA00430HLA00432_HLA02561HLA00432_HLA05526HLA00435_HLA00434HLA00435_HLA01326HLA00435_HLA01902HLA00435_HLA07777HLA00435_HLA07778HLA00437_HLA00433HLA00437_HLA07937HLA00437_HLA00434HLA00437_HLA01326HLA00437_HLA01902HLA00437_HLA07777HLA00437_HLA07778HLA00437_HLA00438HLA00439_HLA00433HLA00439_HLA07937HLA00439_HLA00438HLA00440_HLA00434HLA00440_HLA01326HLA00440_HLA01902HLA00440_HLA07777HLA00440_HLA07778HLA00441_HLA00433HLA00441_HLA07937HLA00441_HLA00438HLA00442_HLA00434HLA00442_HLA01326HLA00442_HLA01902HLA00442_HLA07777HLA00442_HLA07778HLA00444_HLA00436HLA00449_HLA00446HLA00450_HLA00447HLA00456_HLA00430HLA00456_HLA02561HLA00456_HLA05526HLA00456_HLA02766HLA00457_HLA00455HLA00457_HLA02766HLA00458_HLA00455HLA00458_HLA02766HLA00459_HLA00455HLA00459_HLA02766HLA00463_HLA00462HLA00465_HLA00462HLA00468_HLA00467HLA00469_HLA00471HLA00472_HLA00471HLA00473_HLA00467HLA00474_HLA00467HLA00991_HLA00430HLA00991_HLA02561HLA00991_HLA05526HLA01075_HLA03303HLA01076_HLA00413HLA01077_HLA00411HLA01078_HLA00420HLA01078_HLA01328HLA01078_HLA03572HLA01078_HLA08080HLA01079_HLA00434HLA01079_HLA01326HLA01079_HLA01902HLA01079_HLA07777HLA01079_HLA07778HLA01080_HLA00433HLA01080_HLA07937HLA01080_HLA00434HLA01080_HLA01326HLA01080_HLA01902HLA01080_HLA07777HLA01080_HLA07778HLA01080_HLA00438HLA01081_HLA00467HLA01124_HLA00471HLA01136_HLA00446HLA01138_HLA00455HLA01138_HLA02766HLA01145_HLA00454HLA01174_HLA00427HLA01174_HLA03586HLA01238_HLA00445HLA01258_HLA00430HLA01258_HLA02561HLA01301_HLA00430HLA01301_HLA02561HLA01301_HLA05526HLA01311_HLA00420HLA01311_HLA01328HLA01311_HLA03572HLA01311_HLA08080HLA01315_HLA00455HLA01315_HLA02766HLA01322_HLA00445HLA01342_HLA00467HLA01344_HLA00405HLA01355_HLA00411HLA01408_HLA00434HLA01408_HLA01326HLA01408_HLA01902HLA01408_HLA07777HLA01408_HLA07778HLA01424_HLA02438HLA01425_HLA02881HLA01434_HLA00401HLA01469_HLA00462HLA01471_HLA02120HLA01472_HLA02120HLA01581_HLA00410HLA01581_HLA05731HLA01586_HLA00445HLA01588_HLA00433HLA01588_HLA07937HLA01588_HLA00438HLA01602_HLA00427HLA01602_HLA03586HLA01628_HLA00430HLA01628_HLA02561HLA01628_HLA05526HLA01644_HLA00401HLA01645_HLA00420HLA01645_HLA01328HLA01645_HLA03572HLA01645_HLA08080HLA01659_HLA00401HLA01660_HLA00410HLA01660_HLA05731HLA01661_HLA00427HLA01661_HLA03586HLA01662_HLA00434HLA01662_HLA01326HLA01662_HLA01902HLA01662_HLA07777HLA01662_HLA07778HLA01672_HLA01720HLA01673_HLA02120HLA01681_HLA00430HLA01681_HLA02561HLA01705_HLA00476HLA01708_HLA00475HLA01711_HLA00420HLA01711_HLA01328HLA01711_HLA03572HLA01711_HLA08080HLA01715_HLA00405HLA01721_HLA00462HLA01729_HLA00433HLA01729_HLA07937HLA01729_HLA00438HLA01739_HLA00405HLA01787_HLA00454HLA01799_HLA00455HLA01799_HLA02766HLA01824_HLA00430HLA01824_HLA02561HLA01824_HLA05526HLA01825_HLA00420HLA01825_HLA01328HLA01825_HLA03572HLA01825_HLA08080HLA01831_HLA00420HLA01831_HLA01328HLA01831_HLA03572HLA01831_HLA08080HLA01832_HLA00427HLA01832_HLA03586HLA01833_HLA00433HLA01833_HLA07937HLA01833_HLA00438HLA01835_HLA00445HLA01844_HLA00433HLA01844_HLA07937HLA01844_HLA00438HLA01851_HLA00420HLA01851_HLA01328HLA01851_HLA03572HLA01851_HLA08080HLA01853_HLA00420HLA01853_HLA01328HLA01853_HLA03572HLA01853_HLA08080HLA01855_HLA00411HLA01857_HLA00445HLA01859_HLA00420HLA01859_HLA01328HLA01859_HLA03572HLA01859_HLA08080HLA01862_HLA00405HLA01863_HLA00434HLA01863_HLA01326HLA01863_HLA01902HLA01863_HLA07777HLA01863_HLA07778HLA01864_HLA00433HLA01864_HLA07937HLA01864_HLA00438HLA01865_HLA00433HLA01865_HLA07937HLA01865_HLA00438HLA01866_HLA00401HLA01877_HLA00434HLA01877_HLA01326HLA01877_HLA01902HLA01877_HLA07777HLA01877_HLA07778HLA01878_HLA00455HLA01878_HLA02766HLA01879_HLA00446HLA01880_HLA00430HLA01880_HLA02561HLA01880_HLA05526HLA01884_HLA00467HLA01885_HLA00455HLA01885_HLA02766HLA01906_HLA01412HLA01907_HLA00427HLA01907_HLA03586HLA01908_HLA00433HLA01908_HLA07937HLA01908_HLA00434HLA01908_HLA01326HLA01908_HLA01902HLA01908_HLA07777HLA01908_HLA07778HLA01908_HLA00438HLA01909_HLA00471HLA01925_HLA00411HLA01935_HLA00454HLA01961_HLA00433HLA01961_HLA07937HLA01961_HLA00438HLA01969_HLA00455HLA01969_HLA02766HLA01998_HLA00427HLA01998_HLA03586HLA02010_HLA00434HLA02010_HLA01326HLA02010_HLA01902HLA02010_HLA07777HLA02010_HLA07778HLA02041_HLA00475HLA02044_HLA00401HLA02086_HLA00420HLA02086_HLA01328HLA02086_HLA03572HLA02086_HLA08080HLA02087_HLA00462HLA02123_HLA00401HLA02133_HLA00413HLA02148_HLA00427HLA02148_HLA03586HLA02178_HLA00430HLA02178_HLA02561HLA02193_HLA00423HLA02205_HLA00433HLA02205_HLA07937HLA02205_HLA00434HLA02205_HLA01326HLA02205_HLA01902HLA02205_HLA07777HLA02205_HLA07778HLA02205_HLA00438HLA02207_HLA00462HLA02239_HLA00430HLA02239_HLA02561HLA02239_HLA05526HLA02240_HLA02120HLA02241_HLA00420HLA02241_HLA01328HLA02241_HLA03572HLA02241_HLA08080HLA02242_HLA00475HLA02253_HLA00462HLA02292_HLA00427HLA02292_HLA03586HLA02293_HLA00433HLA02293_HLA07937HLA02293_HLA00438HLA02302_HLA00448HLA02303_HLA00475HLA02304_HLA00454HLA02319_HLA00481HLA02357_HLA00454HLA02375_HLA00411HLA02380_HLA00434HLA02380_HLA01326HLA02380_HLA01902HLA02380_HLA07777HLA02380_HLA07778HLA02391_HLA00411HLA02396_HLA00467HLA02397_HLA00427HLA02397_HLA03586HLA02408_HLA00427HLA02408_HLA03586HLA02414_HLA00411HLA02422_HLA00433HLA02422_HLA07937HLA02422_HLA00438HLA02423_HLA00405HLA02424_HLA00467HLA02425_HLA00433HLA02425_HLA07937HLA02425_HLA00438HLA02427_HLA00462HLA02428_HLA00455HLA02428_HLA02766HLA02429_HLA00420HLA02429_HLA01328HLA02429_HLA03572HLA02429_HLA08080HLA02430_HLA02120HLA02434_HLA00420HLA02434_HLA01328HLA02434_HLA03572HLA02434_HLA08080HLA02444_HLA00413HLA02445_HLA00447HLA02448_HLA00433HLA02448_HLA07937HLA02459_HLA00434HLA02459_HLA01326HLA02459_HLA01902HLA02459_HLA07777HLA02459_HLA07778HLA02467_HLA00413HLA02469_HLA00401HLA02475_HLA00434HLA02475_HLA01326HLA02475_HLA01902HLA02475_HLA07777HLA02475_HLA07778HLA02478_HLA00401HLA02485_HLA00415HLA02511_HLA00420HLA02511_HLA01328HLA02511_HLA03572HLA02511_HLA08080HLA02522_HLA00413HLA02523_HLA00433HLA02523_HLA07937HLA02523_HLA00438HLA02525_HLA00420HLA02525_HLA01328HLA02525_HLA03572HLA02525_HLA08080HLA02526_HLA00413HLA02527_HLA00454HLA02559_HLA00405HLA02564_HLA00434HLA02564_HLA01326HLA02564_HLA01902HLA02564_HLA07777HLA02564_HLA07778HLA02567_HLA00411HLA02586_HLA00427HLA02586_HLA03586HLA02593_HLA03589HLA02594_HLA00415HLA02598_HLA00433HLA02598_HLA07937HLA02598_HLA00438HLA02599_HLA00413HLA02600_HLA00413HLA02611_HLA00433HLA02611_HLA07937HLA02611_HLA00438HLA02614_HLA00446HLA02617_HLA00411HLA02621_HLA00420HLA02621_HLA01328HLA02621_HLA03572HLA02621_HLA08080HLA02622_HLA00420HLA02622_HLA01328HLA02622_HLA03572HLA02622_HLA08080HLA02641_HLA00430HLA02641_HLA02561HLA02641_HLA05526HLA02648_HLA00411HLA02670_HLA00401HLA02680_HLA00434HLA02680_HLA01326HLA02680_HLA01902HLA02680_HLA07777HLA02680_HLA07778HLA02681_HLA00413HLA02686_HLA00476HLA02697_HLA00433HLA02697_HLA07937HLA02697_HLA00434HLA02697_HLA01326HLA02697_HLA01902HLA02697_HLA07777HLA02697_HLA07778HLA02697_HLA00438HLA02708_HLA00430HLA02708_HLA02561HLA02708_HLA05526HLA02709_HLA00433HLA02709_HLA07937HLA02709_HLA00438HLA02715_HLA00410HLA02715_HLA05731HLA02729_HLA00413HLA02730_HLA00436HLA02753_HLA00427HLA02753_HLA03586HLA02758_HLA01412HLA02764_HLA02120HLA02785_HLA00427HLA02785_HLA03586HLA02789_HLA00434HLA02789_HLA01326HLA02789_HLA01902HLA02789_HLA07777HLA02789_HLA07778HLA02791_HLA00455HLA02791_HLA02766HLA02811_HLA00401HLA02812_HLA00401HLA02813_HLA00401HLA02814_HLA00401HLA02815_HLA00401HLA02816_HLA03589HLA02817_HLA00410HLA02817_HLA05731HLA02818_HLA00413HLA02819_HLA00414HLA02820_HLA00413HLA02821_HLA00414HLA02822_HLA00420HLA02822_HLA01328HLA02822_HLA03572HLA02822_HLA08080HLA02824_HLA00420HLA02824_HLA01328HLA02824_HLA03572HLA02824_HLA08080HLA02831_HLA00420HLA02831_HLA01328HLA02831_HLA03572HLA02831_HLA08080HLA02832_HLA00430HLA02832_HLA02561HLA02832_HLA05526HLA02833_HLA00430HLA02833_HLA02561HLA02833_HLA05526HLA02834_HLA00434HLA02834_HLA01326HLA02834_HLA01902HLA02834_HLA07777HLA02834_HLA07778HLA02835_HLA00434HLA02835_HLA01326HLA02835_HLA01902HLA02835_HLA07777HLA02835_HLA07778HLA02836_HLA00467HLA02837_HLA00471HLA02839_HLA00483HLA02842_HLA00455HLA02842_HLA02766HLA02843_HLA00411HLA02868_HLA00475HLA02927_HLA00413HLA02928_HLA00467HLA02947_HLA00401HLA02979_HLA01856HLA02993_HLA02881HLA02994_HLA00411HLA02998_HLA00413HLA03012_HLA00433HLA03012_HLA07937HLA03012_HLA00438HLA03013_HLA00434HLA03013_HLA01326HLA03013_HLA01902HLA03013_HLA07777HLA03013_HLA07778HLA03017_HLA00446HLA03024_HLA00405HLA03027_HLA00413HLA03048_HLA00413HLA03077_HLA00420HLA03077_HLA01328HLA03077_HLA03572HLA03077_HLA08080HLA03079_HLA00405HLA03081_HLA00405HLA03106_HLA00420HLA03106_HLA01328HLA03106_HLA03572HLA03106_HLA08080HLA03107_HLA00433HLA03107_HLA07937HLA03107_HLA00434HLA03107_HLA01326HLA03107_HLA01902HLA03107_HLA07777HLA03107_HLA07778HLA03107_HLA00438HLA03108_HLA00467HLA03115_HLA00475HLA03121_HLA00462HLA03127_HLA00455HLA03127_HLA02766HLA03128_HLA00420HLA03128_HLA01328HLA03128_HLA03572HLA03128_HLA08080HLA03139_HLA00433HLA03139_HLA07937HLA03139_HLA00438HLA03146_HLA00467HLA03163_HLA00413HLA03212_HLA00427HLA03212_HLA03586HLA03214_HLA00420HLA03214_HLA01328HLA03214_HLA03572HLA03214_HLA08080HLA03219_HLA00427HLA03219_HLA03586HLA03226_HLA00420HLA03226_HLA01328HLA03226_HLA03572HLA03226_HLA08080HLA03232_HLA00434HLA03232_HLA01326HLA03232_HLA01902HLA03232_HLA07777HLA03232_HLA07778HLA03233_HLA00401HLA03238_HLA00475HLA03239_HLA00434HLA03239_HLA01326HLA03239_HLA01902HLA03239_HLA07777HLA03239_HLA07778HLA03242_HLA00413HLA03252_HLA00405HLA03280_HLA00445HLA03298_HLA00433HLA03298_HLA07937HLA03298_HLA00438HLA03310_HLA00434HLA03310_HLA01326HLA03310_HLA01902HLA03310_HLA07777HLA03310_HLA07778HLA03362_HLA00411HLA03363_HLA00401HLA03364_HLA00420HLA03364_HLA01328HLA03364_HLA03572HLA03364_HLA08080HLA03365_HLA00433HLA03365_HLA07937HLA03402_HLA00411HLA03404_HLA00420HLA03404_HLA01328HLA03404_HLA03572HLA03404_HLA08080HLA03405_HLA00405HLA03414_HLA00433HLA03414_HLA07937HLA03414_HLA00438HLA03415_HLA00464HLA03419_HLA00433HLA03419_HLA07937HLA03420_HLA00446HLA03425_HLA00476HLA03429_HLA00430HLA03429_HLA02561HLA03429_HLA05526HLA03430_HLA00420HLA03430_HLA01328HLA03430_HLA03572HLA03430_HLA08080HLA03436_HLA00433HLA03436_HLA07937HLA03436_HLA00438HLA03437_HLA00420HLA03437_HLA01328HLA03437_HLA03572HLA03437_HLA08080HLA03438_HLA00427HLA03438_HLA03586HLA03438_HLA00446HLA03439_HLA00434HLA03439_HLA01326HLA03439_HLA01902HLA03439_HLA07777HLA03439_HLA07778HLA03440_HLA00446HLA03444_HLA00434HLA03444_HLA01326HLA03444_HLA01902HLA03444_HLA07777HLA03444_HLA07778HLA03445_HLA00401HLA03455_HLA00462HLA03459_HLA00434HLA03459_HLA01326HLA03459_HLA01902HLA03459_HLA07777HLA03459_HLA07778HLA03477_HLA00436HLA03482_HLA00446HLA03504_HLA00420HLA03504_HLA01328HLA03504_HLA03572HLA03504_HLA08080HLA03515_HLA00434HLA03515_HLA01326HLA03515_HLA01902HLA03515_HLA07777HLA03515_HLA07778HLA03517_HLA00427HLA03517_HLA03586HLA03526_HLA00430HLA03526_HLA02561HLA03526_HLA05526HLA03527_HLA00420HLA03527_HLA01328HLA03527_HLA03572HLA03527_HLA08080HLA03531_HLA00427HLA03531_HLA03586HLA03538_HLA00436HLA03539_HLA00405HLA03544_HLA00411HLA03545_HLA00481HLA03546_HLA00433HLA03546_HLA07937HLA03546_HLA00438HLA03563_HLA00427HLA03563_HLA03586HLA03598_HLA00401HLA03619_HLA00454HLA03624_HLA00430HLA03624_HLA02561HLA03624_HLA05526HLA03634_HLA00427HLA03634_HLA03586HLA03638_HLA00434HLA03638_HLA01326HLA03638_HLA01902HLA03638_HLA07777HLA03638_HLA07778HLA03678_HLA00420HLA03678_HLA01328HLA03678_HLA03572HLA03678_HLA08080HLA03681_HLA00427HLA03681_HLA03586HLA03682_HLA00430HLA03682_HLA02561HLA03682_HLA05526HLA03687_HLA00413HLA03696_HLA00446HLA03697_HLA00430HLA03697_HLA02561HLA03697_HLA05526HLA03698_HLA00436HLA03699_HLA00420HLA03699_HLA01328HLA03699_HLA03572HLA03699_HLA08080HLA03700_HLA00433HLA03700_HLA07937HLA03700_HLA00438HLA03701_HLA00433HLA03701_HLA07937HLA03701_HLA00438HLA03702_HLA00433HLA03702_HLA07937HLA03702_HLA00438HLA03703_HLA00434HLA03703_HLA01326HLA03703_HLA01902HLA03703_HLA07777HLA03703_HLA07778HLA03704_HLA00405HLA03705_HLA00405HLA03706_HLA00401HLA03707_HLA00401HLA03713_HLA00402HLA03723_HLA00413HLA03724_HLA00411HLA03725_HLA00411HLA03726_HLA00475HLA03727_HLA00430HLA03727_HLA02561HLA03727_HLA05526HLA03728_HLA00405HLA03729_HLA00413HLA03730_HLA00401HLA03731_HLA00405HLA03732_HLA00411HLA03733_HLA00411HLA03734_HLA00420HLA03734_HLA01328HLA03734_HLA03572HLA03734_HLA08080HLA03735_HLA00420HLA03735_HLA01328HLA03735_HLA03572HLA03735_HLA08080HLA03736_HLA00420HLA03736_HLA01328HLA03736_HLA03572HLA03736_HLA08080HLA03737_HLA00411HLA03738_HLA00475HLA03739_HLA00405HLA03758_HLA00447HLA03767_HLA00446HLA03801_HLA00405HLA03802_HLA00420HLA03802_HLA01328HLA03802_HLA03572HLA03802_HLA08080HLA03805_HLA00420HLA03805_HLA01328HLA03805_HLA03572HLA03805_HLA08080HLA03813_HLA00471HLA03818_HLA00445HLA03819_HLA00433HLA03819_HLA07937HLA03819_HLA00438HLA03820_HLA00462HLA03826_HLA00405HLA03827_HLA00411HLA03828_HLA00410HLA03828_HLA05731HLA03830_HLA00401HLA03992_HLA00420HLA03992_HLA01328HLA03992_HLA03572HLA03992_HLA08080HLA04019_HLA00401HLA04021_HLA00434HLA04021_HLA01326HLA04021_HLA01902HLA04021_HLA07777HLA04021_HLA07778HLA04129_HLA00455HLA04129_HLA02766HLA04130_HLA02943HLA04133_HLA00427HLA04133_HLA03586HLA04254_HLA00420HLA04254_HLA01328HLA04254_HLA03572HLA04254_HLA08080HLA04255_HLA00413HLA04256_HLA00413HLA04257_HLA00413HLA04258_HLA00401HLA04259_HLA00413HLA04260_HLA00413HLA04261_HLA00413HLA04262_HLA00411HLA04263_HLA00413HLA04264_HLA00411HLA04265_HLA00411HLA04266_HLA00411HLA04267_HLA00413HLA04268_HLA00411HLA04269_HLA00411HLA04270_HLA00411HLA04271_HLA00413HLA04272_HLA00413HLA04273_HLA00410HLA04273_HLA05731HLA04274_HLA00413HLA04275_HLA00401HLA04276_HLA00420HLA04276_HLA01328HLA04276_HLA03572HLA04276_HLA08080HLA04277_HLA00405HLA04278_HLA00413HLA04279_HLA00413HLA04280_HLA00413HLA04281_HLA00411HLA04282_HLA00411HLA04283_HLA00411HLA04284_HLA00405HLA04285_HLA00410HLA04285_HLA05731HLA04286_HLA00420HLA04286_HLA01328HLA04286_HLA03572HLA04286_HLA08080HLA04287_HLA00410HLA04287_HLA05731HLA04288_HLA00411HLA04289_HLA00401HLA04290_HLA00401HLA04291_HLA00430HLA04291_HLA02561HLA04291_HLA05526HLA04292_HLA00430HLA04292_HLA02561HLA04292_HLA05526HLA04293_HLA00427HLA04293_HLA03586HLA04294_HLA00430HLA04294_HLA02561HLA04294_HLA05526HLA04295_HLA00430HLA04295_HLA02561HLA04295_HLA05526HLA04296_HLA00427HLA04296_HLA03586HLA04297_HLA00427HLA04297_HLA03586HLA04298_HLA00420HLA04298_HLA01328HLA04298_HLA03572HLA04298_HLA08080HLA04299_HLA00430HLA04299_HLA02561HLA04299_HLA05526HLA04300_HLA00420HLA04300_HLA01328HLA04300_HLA03572HLA04300_HLA08080HLA04301_HLA00420HLA04301_HLA01328HLA04301_HLA03572HLA04301_HLA08080HLA04302_HLA00427HLA04302_HLA03586HLA04303_HLA00420HLA04303_HLA01328HLA04303_HLA03572HLA04303_HLA08080HLA04304_HLA00427HLA04304_HLA03586HLA04305_HLA00427HLA04305_HLA03586HLA04306_HLA00427HLA04306_HLA03586HLA04307_HLA00430HLA04307_HLA02561HLA04307_HLA05526HLA04308_HLA00427HLA04308_HLA03586HLA04309_HLA00420HLA04309_HLA01328HLA04309_HLA03572HLA04309_HLA08080HLA04310_HLA00427HLA04310_HLA03586HLA04312_HLA00471HLA04313_HLA00455HLA04313_HLA02766HLA04314_HLA00434HLA04314_HLA01326HLA04314_HLA01902HLA04314_HLA07777HLA04314_HLA07778HLA04315_HLA00434HLA04315_HLA01326HLA04315_HLA01902HLA04315_HLA07777HLA04315_HLA07778HLA04316_HLA00455HLA04316_HLA02766HLA04317_HLA00434HLA04317_HLA01326HLA04317_HLA01902HLA04317_HLA07777HLA04317_HLA07778HLA04318_HLA00433HLA04318_HLA07937HLA04318_HLA00438HLA04319_HLA00446HLA04320_HLA00434HLA04320_HLA01326HLA04320_HLA01902HLA04320_HLA07777HLA04320_HLA07778HLA04321_HLA00475HLA04322_HLA00433HLA04322_HLA07937HLA04322_HLA00438HLA04323_HLA00434HLA04323_HLA01326HLA04323_HLA01902HLA04323_HLA07777HLA04323_HLA07778HLA04324_HLA00434HLA04324_HLA01326HLA04324_HLA01902HLA04324_HLA07777HLA04324_HLA07778HLA04325_HLA00433HLA04325_HLA07937HLA04325_HLA00438HLA04326_HLA00455HLA04326_HLA02766HLA04327_HLA00462HLA04328_HLA00433HLA04328_HLA07937HLA04328_HLA00438HLA04329_HLA00433HLA04329_HLA07937HLA04329_HLA00438HLA04330_HLA00433HLA04330_HLA07937HLA04330_HLA00438HLA04331_HLA00434HLA04331_HLA01326HLA04331_HLA01902HLA04331_HLA07777HLA04331_HLA07778HLA04332_HLA00446HLA04332_HLA03975HLA04333_HLA00475HLA04334_HLA00454HLA04335_HLA00433HLA04335_HLA07937HLA04335_HLA00438HLA04336_HLA00455HLA04336_HLA02766HLA04337_HLA00455HLA04337_HLA02766HLA04338_HLA00433HLA04338_HLA07937HLA04338_HLA00438HLA04339_HLA00434HLA04339_HLA01326HLA04339_HLA01902HLA04339_HLA07777HLA04339_HLA07778HLA04340_HLA00433HLA04340_HLA07937HLA04340_HLA00438HLA04341_HLA00462HLA04342_HLA00434HLA04342_HLA01326HLA04342_HLA01902HLA04342_HLA07777HLA04342_HLA07778HLA04343_HLA00433HLA04343_HLA07937HLA04343_HLA00438HLA04344_HLA00434HLA04344_HLA01326HLA04344_HLA01902HLA04344_HLA07777HLA04344_HLA07778HLA04345_HLA00446HLA04346_HLA00475HLA04347_HLA00434HLA04347_HLA01326HLA04347_HLA01902HLA04347_HLA07777HLA04347_HLA07778HLA04348_HLA00433HLA04348_HLA07937HLA04348_HLA00438HLA04391_HLA00427HLA04391_HLA03586HLA04392_HLA00446HLA04393_HLA00446HLA04394_HLA00427HLA04394_HLA03586HLA04395_HLA00420HLA04395_HLA01328HLA04395_HLA03572HLA04395_HLA08080HLA04396_HLA01889HLA04399_HLA00992HLA04570_HLA00402HLA04574_HLA00420HLA04574_HLA01328HLA04574_HLA03572HLA04574_HLA08080HLA04579_HLA02404HLA04583_HLA00446HLA04583_HLA03975HLA04587_HLA00427HLA04587_HLA03586HLA04588_HLA00433HLA04588_HLA07937HLA04588_HLA00438HLA04589_HLA00413HLA04590_HLA00420HLA04590_HLA01328HLA04590_HLA03572HLA04590_HLA08080HLA04591_HLA00455HLA04591_HLA02766HLA04592_HLA00454HLA04593_HLA00405HLA04594_HLA00433HLA04594_HLA07937HLA04594_HLA00438HLA04595_HLA00413HLA04596_HLA00427HLA04596_HLA03586HLA04597_HLA01889HLA04598_HLA00471HLA04599_HLA00475HLA04600_HLA00455HLA04600_HLA02766HLA04601_HLA00434HLA04601_HLA01326HLA04601_HLA01902HLA04601_HLA07777HLA04601_HLA07778HLA04602_HLA00455HLA04602_HLA02766HLA04603_HLA00413HLA04604_HLA00476HLA04605_HLA00410HLA04605_HLA05731HLA04606_HLA00401HLA04607_HLA00433HLA04607_HLA07937HLA04607_HLA00438HLA04608_HLA00427HLA04608_HLA03586HLA04609_HLA00434HLA04609_HLA01326HLA04609_HLA01902HLA04609_HLA07777HLA04609_HLA07778HLA04610_HLA00420HLA04610_HLA01328HLA04610_HLA03572HLA04610_HLA08080HLA04611_HLA00420HLA04611_HLA01328HLA04611_HLA03572HLA04611_HLA08080HLA04612_HLA00434HLA04612_HLA01326HLA04612_HLA01902HLA04612_HLA07777HLA04612_HLA07778HLA04616_HLA00405HLA04617_HLA00420HLA04617_HLA01328HLA04617_HLA03572HLA04617_HLA08080HLA04618_HLA00413HLA04619_HLA00462HLA04620_HLA00454HLA04621_HLA00405HLA04622_HLA00413HLA04623_HLA00481HLA04624_HLA00467HLA04625_HLA00420HLA04625_HLA01328HLA04625_HLA03572HLA04625_HLA08080HLA04626_HLA00420HLA04626_HLA01328HLA04626_HLA03572HLA04626_HLA08080HLA04627_HLA00475HLA04628_HLA00481HLA04629_HLA00414HLA04630_HLA00434HLA04630_HLA01326HLA04630_HLA01902HLA04630_HLA07777HLA04630_HLA07778HLA04631_HLA00481HLA04632_HLA00476HLA04633_HLA00411HLA04638_HLA00430HLA04638_HLA02561HLA04639_HLA00467HLA04677_HLA00427HLA04677_HLA03586HLA04679_HLA00454HLA04693_HLA00471HLA04694_HLA00462HLA04695_HLA00420HLA04695_HLA01328HLA04695_HLA03572HLA04695_HLA08080HLA04696_HLA00420HLA04696_HLA01328HLA04696_HLA03572HLA04696_HLA08080HLA04697_HLA00430HLA04697_HLA02561HLA04698_HLA00475HLA04699_HLA00405HLA04700_HLA00430HLA04700_HLA02561HLA04700_HLA05526HLA04701_HLA00427HLA04701_HLA03586HLA04702_HLA00413HLA04731_HLA00401HLA04736_HLA00413HLA04745_HLA00430HLA04745_HLA02561HLA04745_HLA05526HLA04756_HLA00401HLA04757_HLA00455HLA04757_HLA02766HLA04758_HLA00411HLA04759_HLA00420HLA04759_HLA01328HLA04759_HLA03572HLA04759_HLA08080HLA04763_HLA00420HLA04763_HLA01328HLA04763_HLA03572HLA04763_HLA08080HLA04764_HLA00405HLA04764_HLA03589HLA04765_HLA02120HLA04766_HLA00476HLA04767_HLA00475HLA04777_HLA00413HLA04778_HLA00462HLA04779_HLA00471HLA04780_HLA00430HLA04780_HLA02561HLA04780_HLA05526HLA04784_HLA00462HLA04794_HLA00411HLA04798_HLA00427HLA04798_HLA03586HLA04799_HLA00427HLA04799_HLA03586HLA04800_HLA00427HLA04800_HLA03586HLA04801_HLA00427HLA04801_HLA03586HLA04802_HLA00427HLA04802_HLA03586HLA04803_HLA00427HLA04803_HLA03586HLA04822_HLA00410HLA04822_HLA05731HLA04823_HLA00405HLA04824_HLA00434HLA04824_HLA01326HLA04824_HLA01902HLA04824_HLA07777HLA04824_HLA07778HLA04825_HLA00455HLA04825_HLA02766HLA04826_HLA00462HLA04827_HLA00420HLA04827_HLA01328HLA04827_HLA03572HLA04827_HLA08080HLA04828_HLA00430HLA04828_HLA02561HLA04828_HLA05526HLA04829_HLA00476HLA04830_HLA00405HLA04831_HLA00467HLA04832_HLA00427HLA04832_HLA03586HLA04833_HLA00433HLA04833_HLA07937HLA04833_HLA00438HLA04834_HLA00455HLA04834_HLA02766HLA04835_HLA00430HLA04835_HLA02561HLA04835_HLA05526HLA04836_HLA00455HLA04836_HLA02766HLA04837_HLA00430HLA04837_HLA02561HLA04837_HLA05526HLA04838_HLA00420HLA04838_HLA01328HLA04838_HLA03572HLA04838_HLA08080HLA04839_HLA00476HLA04840_HLA00455HLA04840_HLA02766HLA04841_HLA00420HLA04841_HLA01328HLA04841_HLA03572HLA04841_HLA08080HLA04842_HLA00420HLA04842_HLA01328HLA04842_HLA03572HLA04842_HLA08080HLA04843_HLA00420HLA04843_HLA01328HLA04843_HLA03572HLA04843_HLA08080HLA04844_HLA00430HLA04844_HLA02561HLA04844_HLA05526HLA04845_HLA00405HLA04851_HLA00420HLA04851_HLA01328HLA04851_HLA03572HLA04851_HLA08080HLA04852_HLA00401HLA04858_HLA00454HLA04974_HLA00434HLA04974_HLA01326HLA04974_HLA01902HLA04974_HLA07777HLA04974_HLA07778HLA04982_HLA00436HLA04983_HLA00434HLA04983_HLA01326HLA04983_HLA01902HLA04983_HLA07777HLA04983_HLA07778HLA04995_HLA00433HLA04995_HLA07937HLA04995_HLA00438HLA04996_HLA00433HLA04996_HLA07937HLA04996_HLA00438HLA05012_HLA00434HLA05012_HLA01326HLA05012_HLA01902HLA05012_HLA07777HLA05012_HLA07778HLA05013_HLA00433HLA05013_HLA07937HLA05013_HLA00438HLA05014_HLA00434HLA05014_HLA01326HLA05014_HLA01902HLA05014_HLA07777HLA05014_HLA07778HLA05015_HLA00433HLA05015_HLA07937HLA05015_HLA00438HLA05015_HLA01720HLA05016_HLA00433HLA05016_HLA07937HLA05016_HLA00438HLA05017_HLA00433HLA05017_HLA07937HLA05017_HLA00438HLA05022_HLA00433HLA05022_HLA07937HLA05022_HLA00438HLA05023_HLA00433HLA05023_HLA07937HLA05023_HLA00438HLA05024_HLA00433HLA05024_HLA07937HLA05024_HLA00438HLA05025_HLA00434HLA05025_HLA01326HLA05025_HLA01902HLA05025_HLA07777HLA05025_HLA07778HLA05026_HLA00433HLA05026_HLA07937HLA05026_HLA00438HLA05027_HLA00433HLA05027_HLA07937HLA05027_HLA00438HLA05028_HLA00434HLA05028_HLA01326HLA05028_HLA01902HLA05028_HLA07777HLA05028_HLA07778HLA05029_HLA00433HLA05029_HLA07937HLA05029_HLA00438HLA05030_HLA00433HLA05030_HLA07937HLA05030_HLA00438HLA05031_HLA00433HLA05031_HLA07937HLA05031_HLA00438HLA05032_HLA00434HLA05032_HLA01326HLA05032_HLA01902HLA05032_HLA07777HLA05032_HLA07778HLA05033_HLA00433HLA05033_HLA07937HLA05033_HLA00438HLA05034_HLA00434HLA05034_HLA01326HLA05034_HLA01902HLA05034_HLA07777HLA05034_HLA07778HLA05035_HLA00433HLA05035_HLA07937HLA05035_HLA00438HLA05036_HLA00434HLA05036_HLA01326HLA05036_HLA01902HLA05036_HLA07777HLA05036_HLA07778HLA05064_HLA00434HLA05064_HLA01326HLA05064_HLA01902HLA05064_HLA07777HLA05064_HLA07778HLA05065_HLA00434HLA05065_HLA01326HLA05065_HLA01902HLA05065_HLA07777HLA05065_HLA07778HLA05066_HLA00433HLA05066_HLA07937HLA05066_HLA00438HLA05067_HLA00433HLA05067_HLA07937HLA05067_HLA00438HLA05068_HLA00434HLA05068_HLA01326HLA05068_HLA01902HLA05068_HLA07777HLA05068_HLA07778HLA05069_HLA00433HLA05069_HLA07937HLA05069_HLA00438HLA05070_HLA00433HLA05070_HLA07937HLA05070_HLA00438HLA05071_HLA00434HLA05071_HLA01326HLA05071_HLA01902HLA05071_HLA07777HLA05071_HLA07778HLA05072_HLA00433HLA05072_HLA07937HLA05072_HLA00438HLA05073_HLA00434HLA05073_HLA01326HLA05073_HLA01902HLA05073_HLA07777HLA05073_HLA07778HLA05074_HLA00434HLA05074_HLA01326HLA05074_HLA01902HLA05074_HLA07777HLA05074_HLA07778HLA05075_HLA00434HLA05075_HLA01326HLA05075_HLA01902HLA05075_HLA07777HLA05075_HLA07778HLA05076_HLA00434HLA05076_HLA01326HLA05076_HLA01902HLA05076_HLA07777HLA05076_HLA07778HLA05077_HLA00436HLA05079_HLA00436HLA05080_HLA00434HLA05080_HLA01326HLA05080_HLA01902HLA05080_HLA07777HLA05080_HLA07778HLA05081_HLA00434HLA05081_HLA01326HLA05081_HLA01902HLA05081_HLA07777HLA05081_HLA07778HLA05082_HLA00434HLA05082_HLA01326HLA05082_HLA01902HLA05082_HLA07777HLA05082_HLA07778HLA05083_HLA00434HLA05083_HLA01326HLA05083_HLA01902HLA05083_HLA07777HLA05083_HLA07778HLA05089_HLA00433HLA05089_HLA07937HLA05089_HLA00438HLA05090_HLA00433HLA05090_HLA07937HLA05090_HLA00438HLA05111_HLA00411HLA05115_HLA00471HLA05119_HLA00462HLA05120_HLA00401HLA05122_HLA01412HLA05122_HLA00475HLA05124_HLA00413HLA05130_HLA00401HLA05138_HLA00434HLA05138_HLA01326HLA05138_HLA01902HLA05138_HLA07777HLA05138_HLA07778HLA05139_HLA02120HLA05158_HLA00467HLA05159_HLA00434HLA05159_HLA01326HLA05159_HLA01902HLA05159_HLA07777HLA05159_HLA07778HLA05160_HLA00467HLA05161_HLA02120HLA05162_HLA00411HLA05163_HLA00475HLA05164_HLA00430HLA05164_HLA02561HLA05164_HLA05526HLA05165_HLA00420HLA05165_HLA01328HLA05165_HLA03572HLA05165_HLA08080HLA05166_HLA00420HLA05166_HLA01328HLA05166_HLA03572HLA05166_HLA08080HLA05167_HLA00420HLA05167_HLA01328HLA05167_HLA03572HLA05167_HLA08080HLA05168_HLA00430HLA05168_HLA02561HLA05168_HLA05526HLA05169_HLA00410HLA05169_HLA05731HLA05170_HLA00420HLA05170_HLA01328HLA05170_HLA03572HLA05170_HLA08080HLA05171_HLA00413HLA05172_HLA00455HLA05172_HLA02766HLA05173_HLA00420HLA05173_HLA01328HLA05173_HLA03572HLA05173_HLA08080HLA05174_HLA00430HLA05174_HLA02561HLA05174_HLA05526HLA05175_HLA00420HLA05175_HLA01328HLA05175_HLA03572HLA05175_HLA08080HLA05176_HLA00430HLA05176_HLA02561HLA05176_HLA05526HLA05177_HLA00481HLA05178_HLA00454HLA05178_HLA02766HLA05179_HLA00475HLA05180_HLA00446HLA05181_HLA00467HLA05182_HLA00475HLA05183_HLA00420HLA05183_HLA01328HLA05183_HLA03572HLA05183_HLA08080HLA05184_HLA00430HLA05184_HLA02561HLA05184_HLA05526HLA05185_HLA00454HLA05186_HLA00405HLA05187_HLA00455HLA05187_HLA02766HLA05188_HLA00446HLA05188_HLA03975HLA05189_HLA00405HLA05190_HLA00434HLA05190_HLA01326HLA05190_HLA01902HLA05190_HLA07777HLA05190_HLA07778HLA05191_HLA00420HLA05191_HLA01328HLA05191_HLA03572HLA05191_HLA08080HLA05192_HLA00430HLA05192_HLA02561HLA05192_HLA05526HLA05194_HLA00462HLA05195_HLA00430HLA05195_HLA02561HLA05196_HLA00446HLA05197_HLA00413HLA05198_HLA00467HLA05199_HLA00455HLA05199_HLA02766HLA05200_HLA00467HLA05201_HLA00405HLA05202_HLA00413HLA05203_HLA00455HLA05203_HLA02766HLA05204_HLA00454HLA05205_HLA00454HLA05206_HLA00420HLA05206_HLA01328HLA05206_HLA03572HLA05206_HLA08080HLA05207_HLA00430HLA05207_HLA02561HLA05207_HLA05526HLA05208_HLA00476HLA05209_HLA00401HLA05210_HLA00405HLA05211_HLA00481HLA05212_HLA00455HLA05212_HLA02766HLA05213_HLA00427HLA05213_HLA03586HLA05214_HLA00455HLA05214_HLA02766HLA05215_HLA00411HLA05216_HLA00467HLA05217_HLA00475HLA05218_HLA00420HLA05218_HLA01328HLA05218_HLA03572HLA05218_HLA08080HLA05219_HLA00420HLA05219_HLA01328HLA05219_HLA03572HLA05219_HLA08080HLA05220_HLA00471HLA05221_HLA00433HLA05221_HLA07937HLA05221_HLA00438HLA05309_HLA00446HLA05310_HLA00427HLA05310_HLA03586HLA05311_HLA00405HLA05352_HLA00436HLA05371_HLA00413HLA05382_HLA00427HLA05382_HLA03586HLA05385_HLA00430HLA05385_HLA02561HLA05385_HLA05526HLA05394_HLA00454HLA05395_HLA00446HLA05395_HLA03975HLA05396_HLA00475HLA05397_HLA00430HLA05397_HLA02561HLA05397_HLA05526HLA05403_HLA00420HLA05403_HLA01328HLA05403_HLA03572HLA05403_HLA08080HLA05423_HLA00430HLA05423_HLA02561HLA05521_HLA00475HLA05544_HLA00433HLA05544_HLA07937HLA05544_HLA00438HLA05554_HLA00433HLA05554_HLA07937HLA05554_HLA00438HLA05558_HLA00471HLA05559_HLA00430HLA05559_HLA02561HLA05559_HLA05526HLA05560_HLA00420HLA05560_HLA01328HLA05560_HLA03572HLA05560_HLA08080HLA05564_HLA00434HLA05564_HLA01326HLA05564_HLA01902HLA05564_HLA07777HLA05564_HLA07778HLA05565_HLA00455HLA05565_HLA02766HLA05566_HLA00430HLA05566_HLA02561HLA05566_HLA05526HLA05567_HLA00405HLA05567_HLA02120HLA05568_HLA00481HLA05569_HLA00420HLA05569_HLA01328HLA05569_HLA03572HLA05569_HLA08080HLA05570_HLA00455HLA05570_HLA02766HLA05571_HLA00427HLA05571_HLA03586HLA05572_HLA00427HLA05572_HLA03586HLA05573_HLA00420HLA05573_HLA01328HLA05573_HLA03572HLA05573_HLA08080HLA05574_HLA00401HLA05575_HLA00455HLA05575_HLA02766HLA05576_HLA00430HLA05576_HLA02561HLA05576_HLA05526HLA05577_HLA00475HLA05578_HLA00478HLA05579_HLA00446HLA05580_HLA00434HLA05580_HLA01326HLA05580_HLA01902HLA05580_HLA07777HLA05580_HLA07778HLA05581_HLA00467HLA05582_HLA00405HLA05583_HLA00430HLA05583_HLA02561HLA05583_HLA05526HLA05584_HLA00405HLA05585_HLA00427HLA05585_HLA03586HLA05586_HLA00420HLA05586_HLA01328HLA05586_HLA03572HLA05586_HLA08080HLA05587_HLA00433HLA05587_HLA07937HLA05587_HLA00438HLA05588_HLA00427HLA05588_HLA03586HLA05589_HLA00475HLA05590_HLA00401HLA05591_HLA00446HLA05592_HLA00420HLA05592_HLA01328HLA05592_HLA03572HLA05592_HLA08080HLA05593_HLA00427HLA05593_HLA03586HLA05594_HLA00405HLA05595_HLA00455HLA05595_HLA02766HLA05596_HLA00475HLA05597_HLA00420HLA05597_HLA01328HLA05597_HLA03572HLA05597_HLA08080HLA05598_HLA00430HLA05598_HLA02561HLA05598_HLA05526HLA05599_HLA00420HLA05599_HLA01328HLA05599_HLA03572HLA05599_HLA08080HLA05600_HLA00467HLA05601_HLA00483HLA05602_HLA00430HLA05602_HLA02561HLA05602_HLA05526HLA05603_HLA00433HLA05603_HLA07937HLA05603_HLA00438HLA05604_HLA00420HLA05604_HLA01328HLA05604_HLA03572HLA05604_HLA08080HLA05605_HLA00410HLA05605_HLA05731HLA05606_HLA00405HLA05607_HLA00411HLA05608_HLA00455HLA05608_HLA02766HLA05609_HLA00481HLA05610_HLA00420HLA05610_HLA01328HLA05610_HLA03572HLA05610_HLA08080HLA05612_HLA00434HLA05612_HLA01326HLA05612_HLA01902HLA05612_HLA07777HLA05612_HLA07778HLA05613_HLA00411HLA05614_HLA00467HLA05615_HLA00471HLA05616_HLA00447HLA05617_HLA00430HLA05617_HLA02561HLA05617_HLA05526HLA05618_HLA00405HLA05619_HLA00430HLA05619_HLA02561HLA05619_HLA05526HLA05620_HLA00420HLA05620_HLA01328HLA05620_HLA03572HLA05620_HLA08080HLA05621_HLA00475HLA05623_HLA00455HLA05623_HLA02766HLA05624_HLA00476HLA05625_HLA00467HLA05626_HLA00433HLA05626_HLA07937HLA05626_HLA00438HLA05627_HLA00434HLA05627_HLA01326HLA05627_HLA01902HLA05627_HLA07777HLA05627_HLA07778HLA05732_HLA00434HLA05732_HLA01326HLA05732_HLA01902HLA05732_HLA07777HLA05732_HLA07778HLA05733_HLA00405HLA05734_HLA00430HLA05734_HLA02561HLA05734_HLA05526HLA05735_HLA00405HLA05736_HLA00427HLA05736_HLA03586HLA05737_HLA00430HLA05737_HLA02561HLA05737_HLA05526HLA05738_HLA00475HLA05739_HLA00420HLA05739_HLA01328HLA05739_HLA03572HLA05739_HLA08080HLA05740_HLA00433HLA05740_HLA07937HLA05740_HLA00438HLA05745_HLA00420HLA05745_HLA01328HLA05745_HLA03572HLA05745_HLA08080HLA05746_HLA00411HLA05747_HLA00413HLA05748_HLA00462HLA05749_HLA00464HLA05750_HLA00467HLA05751_HLA00454HLA05752_HLA00401HLA05753_HLA00445HLA05753_HLA00448HLA05754_HLA00401HLA05755_HLA00413HLA05780_HLA00434HLA05780_HLA01326HLA05780_HLA01902HLA05780_HLA07777HLA05780_HLA07778HLA05782_HLA00423HLA05783_HLA00430HLA05783_HLA02561HLA05820_HLA00434HLA05820_HLA01326HLA05820_HLA01902HLA05820_HLA07777HLA05820_HLA07778HLA05837_HLA00455HLA05837_HLA02766HLA05852_HLA00427HLA05852_HLA03586HLA05854_HLA00467HLA05855_HLA00434HLA05855_HLA01326HLA05855_HLA01902HLA05855_HLA07777HLA05855_HLA07778HLA05863_HLA00445HLA05865_HLA00471HLA05871_HLA00455HLA05871_HLA02766HLA05873_HLA00401HLA05874_HLA00446HLA05879_HLA00467HLA05881_HLA00401HLA05882_HLA00411HLA05883_HLA00420HLA05883_HLA01328HLA05883_HLA03572HLA05883_HLA08080HLA05885_HLA00433HLA05885_HLA07937HLA05885_HLA00438HLA05886_HLA00434HLA05886_HLA01326HLA05886_HLA01902HLA05886_HLA07777HLA05886_HLA07778HLA05887_HLA00434HLA05887_HLA01326HLA05887_HLA01902HLA05887_HLA07777HLA05887_HLA07778HLA05890_HLA00445HLA05891_HLA00462HLA05892_HLA00462HLA05920_HLA00434HLA05920_HLA01326HLA05920_HLA01902HLA05920_HLA07777HLA05920_HLA07778HLA05921_HLA00462HLA05937_HLA00434HLA05937_HLA01326HLA05937_HLA01902HLA05937_HLA07777HLA05937_HLA07778HLA05947_HLA00420HLA05947_HLA01328HLA05947_HLA03572HLA05947_HLA08080HLA05966_HLA00420HLA05966_HLA01328HLA05966_HLA03572HLA05966_HLA08080HLA05996_HLA00433HLA05996_HLA07937HLA05996_HLA00438HLA06001_HLA00455HLA06001_HLA02766HLA06002_HLA00471HLA06043_HLA00430HLA06043_HLA02561HLA06048_HLA00433HLA06048_HLA07937HLA06048_HLA00438HLA06054_HLA01843HLA06067_HLA00411HLA06069_HLA00433HLA06069_HLA07937HLA06069_HLA00438HLA06070_HLA00433HLA06070_HLA07937HLA06070_HLA00438HLA06072_HLA00446HLA06074_HLA00413HLA06076_HLA00401HLA06123_HLA00467HLA06124_HLA00405HLA06128_HLA00462HLA06136_HLA00455HLA06136_HLA02766HLA06138_HLA00446HLA06147_HLA00462HLA06163_HLA00401HLA06164_HLA00401HLA06165_HLA00401HLA06166_HLA00401HLA06169_HLA00413HLA06170_HLA00434HLA06170_HLA01326HLA06170_HLA01902HLA06170_HLA07777HLA06170_HLA07778HLA06171_HLA00434HLA06171_HLA01326HLA06171_HLA01902HLA06171_HLA07777HLA06171_HLA07778HLA06173_HLA00445HLA06175_HLA00462HLA06274_HLA00430HLA06274_HLA02561HLA06274_HLA05526HLA06275_HLA00430HLA06275_HLA02561HLA06275_HLA05526HLA06276_HLA00475HLA06277_HLA00433HLA06277_HLA07937HLA06303_HLA00475HLA06305_HLA00401HLA06306_HLA00434HLA06306_HLA01326HLA06306_HLA01902HLA06306_HLA07777HLA06306_HLA07778HLA06310_HLA00410HLA06310_HLA05731HLA06381_HLA00434HLA06381_HLA01326HLA06381_HLA01902HLA06381_HLA07777HLA06381_HLA07778HLA06382_HLA00427HLA06382_HLA03586HLA06383_HLA00427HLA06383_HLA03586HLA06384_HLA00455HLA06384_HLA02766HLA06385_HLA00420HLA06385_HLA01328HLA06385_HLA03572HLA06385_HLA08080HLA06386_HLA00401HLA06387_HLA00434HLA06387_HLA01326HLA06387_HLA01902HLA06387_HLA07777HLA06387_HLA07778HLA06388_HLA00430HLA06388_HLA02561HLA06388_HLA05526HLA06389_HLA00433HLA06389_HLA07937HLA06389_HLA00438HLA06390_HLA00433HLA06390_HLA07937HLA06390_HLA00438HLA06391_HLA00434HLA06391_HLA01326HLA06391_HLA01902HLA06391_HLA07777HLA06391_HLA07778HLA06392_HLA00434HLA06392_HLA01326HLA06392_HLA01902HLA06392_HLA07777HLA06392_HLA07778HLA06393_HLA00446HLA06394_HLA00446HLA06395_HLA00478HLA06396_HLA00455HLA06396_HLA02766HLA06397_HLA00405HLA06398_HLA00413HLA06399_HLA00410HLA06399_HLA05731HLA06400_HLA02356HLA06401_HLA00420HLA06401_HLA01328HLA06401_HLA03572HLA06401_HLA08080HLA06402_HLA00420HLA06402_HLA01328HLA06402_HLA03572HLA06402_HLA08080HLA06403_HLA00420HLA06403_HLA01328HLA06403_HLA03572HLA06403_HLA08080HLA06404_HLA00420HLA06404_HLA01328HLA06404_HLA03572HLA06404_HLA08080HLA06405_HLA00401HLA06406_HLA00430HLA06406_HLA02561HLA06406_HLA05526HLA06407_HLA00430HLA06407_HLA02561HLA06407_HLA05526HLA06408_HLA00433HLA06408_HLA07937HLA06408_HLA00438HLA06409_HLA00434HLA06409_HLA01326HLA06409_HLA01902HLA06409_HLA07777HLA06409_HLA07778HLA06410_HLA00434HLA06410_HLA01326HLA06410_HLA01902HLA06410_HLA07777HLA06410_HLA07778HLA06411_HLA00427HLA06411_HLA03586HLA06412_HLA00446HLA06413_HLA00446HLA06414_HLA00455HLA06414_HLA02766HLA06415_HLA00455HLA06415_HLA02766HLA06416_HLA00471HLA06417_HLA00413HLA06418_HLA00411HLA06419_HLA00411HLA06420_HLA00410HLA06420_HLA05731HLA06421_HLA00455HLA06421_HLA02766HLA06422_HLA00420HLA06422_HLA01328HLA06422_HLA03572HLA06422_HLA08080HLA06423_HLA00433HLA06423_HLA07937HLA06423_HLA00438HLA06424_HLA00433HLA06424_HLA07937HLA06424_HLA00438HLA06425_HLA00433HLA06425_HLA07937HLA06425_HLA00438HLA06426_HLA00454HLA06427_HLA00481HLA06428_HLA00445HLA06429_HLA00436HLA06430_HLA00433HLA06430_HLA07937HLA06430_HLA00438HLA06431_HLA00427HLA06431_HLA03586HLA06432_HLA00427HLA06432_HLA03586HLA06433_HLA00475HLA06434_HLA00467HLA06435_HLA00462HLA06436_HLA00420HLA06436_HLA01328HLA06436_HLA03572HLA06436_HLA08080HLA06437_HLA00434HLA06437_HLA01326HLA06437_HLA01902HLA06437_HLA07777HLA06437_HLA07778HLA06438_HLA00476HLA06439_HLA00455HLA06439_HLA02766HLA06440_HLA00430HLA06440_HLA02561HLA06440_HLA05526HLA06441_HLA00430HLA06441_HLA02561HLA06441_HLA05526HLA06442_HLA00430HLA06442_HLA02561HLA06442_HLA05526HLA06443_HLA00483HLA06444_HLA00436HLA06445_HLA00413HLA06446_HLA00420HLA06446_HLA01328HLA06446_HLA03572HLA06446_HLA08080HLA06447_HLA00434HLA06447_HLA01326HLA06447_HLA01902HLA06447_HLA07777HLA06447_HLA07778HLA06448_HLA00475HLA06449_HLA00433HLA06449_HLA07937HLA06449_HLA00434HLA06449_HLA01326HLA06449_HLA01902HLA06449_HLA07777HLA06449_HLA07778HLA06449_HLA00438HLA06450_HLA00475HLA06524_HLA00467HLA06525_HLA00434HLA06525_HLA01326HLA06525_HLA01902HLA06525_HLA07777HLA06525_HLA07778HLA06528_HLA00427HLA06528_HLA03586HLA06532_HLA00420HLA06532_HLA01328HLA06532_HLA03572HLA06532_HLA08080HLA06533_HLA00420HLA06533_HLA01328HLA06533_HLA03572HLA06533_HLA08080HLA06535_HLA00434HLA06535_HLA01326HLA06535_HLA01902HLA06535_HLA07777HLA06535_HLA07778HLA06536_HLA07937HLA06582_HLA00455HLA06582_HLA02766HLA06587_HLA00401HLA06644_HLA00445HLA06655_HLA00434HLA06655_HLA01326HLA06655_HLA01902HLA06655_HLA07777HLA06655_HLA07778HLA06656_HLA00402HLA06662_HLA00434HLA06662_HLA01326HLA06662_HLA01902HLA06662_HLA07777HLA06662_HLA07778HLA06665_HLA00420HLA06665_HLA01328HLA06665_HLA03572HLA06665_HLA08080HLA06704_HLA00401HLA06705_HLA00433HLA06705_HLA07937HLA06705_HLA00438HLA06706_HLA00433HLA06706_HLA07937HLA06706_HLA00438HLA06707_HLA00430HLA06707_HLA02561HLA06707_HLA05526HLA06708_HLA00475HLA06709_HLA00481HLA06710_HLA00405HLA06711_HLA00413HLA06712_HLA00413HLA06713_HLA00413HLA06714_HLA00430HLA06714_HLA02561HLA06714_HLA05526HLA06715_HLA00430HLA06715_HLA02561HLA06715_HLA05526HLA06716_HLA00433HLA06716_HLA07937HLA06716_HLA00438HLA06717_HLA00433HLA06717_HLA07937HLA06717_HLA00438HLA06718_HLA00433HLA06718_HLA07937HLA06718_HLA00438HLA06719_HLA00434HLA06719_HLA01326HLA06719_HLA01902HLA06719_HLA07777HLA06719_HLA07778HLA06720_HLA00427HLA06720_HLA03586HLA06721_HLA00446HLA06722_HLA02605HLA06723_HLA00405HLA06724_HLA00405HLA06725_HLA00467HLA06726_HLA00411HLA06727_HLA00413HLA06728_HLA00413HLA06729_HLA00420HLA06729_HLA01328HLA06729_HLA03572HLA06729_HLA08080HLA06730_HLA00420HLA06730_HLA01328HLA06730_HLA03572HLA06730_HLA08080HLA06731_HLA00401HLA06732_HLA00430HLA06732_HLA02561HLA06732_HLA05526HLA06733_HLA00434HLA06733_HLA01326HLA06733_HLA01902HLA06733_HLA07777HLA06733_HLA07778HLA06734_HLA00430HLA06734_HLA02561HLA06734_HLA05526HLA06735_HLA00434HLA06735_HLA01326HLA06735_HLA01902HLA06735_HLA07777HLA06735_HLA07778HLA06736_HLA00405HLA06737_HLA00420HLA06737_HLA01328HLA06737_HLA03572HLA06737_HLA08080HLA06778_HLA00475HLA06824_HLA00436HLA06828_HLA00434HLA06828_HLA01326HLA06828_HLA01902HLA06828_HLA07777HLA06828_HLA07778HLA06890_HLA00475HLA06894_HLA00413HLA06896_HLA00433HLA06896_HLA07937HLA06896_HLA00438HLA06897_HLA00455HLA06897_HLA02766HLA06898_HLA00405HLA06902_HLA00433HLA06902_HLA07937HLA06902_HLA00438HLA07005_HLA00405HLA07006_HLA00411HLA07007_HLA00411HLA07008_HLA00410HLA07008_HLA05731HLA07009_HLA00420HLA07009_HLA01328HLA07009_HLA03572HLA07009_HLA08080HLA07010_HLA00420HLA07010_HLA01328HLA07010_HLA03572HLA07010_HLA08080HLA07011_HLA00427HLA07011_HLA03586HLA07012_HLA00405HLA07013_HLA00411HLA07014_HLA00413HLA07015_HLA02881HLA07016_HLA00411HLA07017_HLA00420HLA07017_HLA01328HLA07017_HLA03572HLA07017_HLA08080HLA07018_HLA00420HLA07018_HLA01328HLA07018_HLA03572HLA07018_HLA08080HLA07019_HLA00420HLA07019_HLA01328HLA07019_HLA03572HLA07019_HLA08080HLA07020_HLA02120HLA07021_HLA00414HLA07022_HLA00420HLA07022_HLA01328HLA07022_HLA03572HLA07022_HLA08080HLA07023_HLA00420HLA07023_HLA01328HLA07023_HLA03572HLA07023_HLA08080HLA07024_HLA00411HLA07025_HLA00411HLA07026_HLA00420HLA07026_HLA01328HLA07026_HLA03572HLA07026_HLA08080HLA07027_HLA00411HLA07028_HLA00427HLA07028_HLA03586HLA07029_HLA00411HLA07030_HLA00420HLA07030_HLA01328HLA07030_HLA03572HLA07030_HLA08080HLA07031_HLA00427HLA07031_HLA03586HLA07036_HLA00413HLA07045_HLA00433HLA07045_HLA07937HLA07045_HLA00438HLA07046_HLA00430HLA07046_HLA02561HLA07046_HLA05526HLA07047_HLA00434HLA07047_HLA01326HLA07047_HLA01902HLA07047_HLA07777HLA07047_HLA07778HLA07048_HLA00476HLA07049_HLA00467HLA07050_HLA00446HLA07051_HLA00434HLA07051_HLA01326HLA07051_HLA01902HLA07051_HLA07777HLA07051_HLA07778HLA07052_HLA00427HLA07052_HLA03586HLA07053_HLA00446HLA07053_HLA03975HLA07054_HLA00475HLA07055_HLA00455HLA07055_HLA02766HLA07056_HLA00467HLA07057_HLA00436HLA07058_HLA00433HLA07058_HLA07937HLA07058_HLA00438HLA07059_HLA00433HLA07059_HLA07937HLA07059_HLA00438HLA07060_HLA00434HLA07060_HLA01326HLA07060_HLA01902HLA07060_HLA07777HLA07060_HLA07778HLA07061_HLA00434HLA07061_HLA01326HLA07061_HLA01902HLA07061_HLA07777HLA07061_HLA07778HLA07062_HLA00455HLA07062_HLA02766HLA07063_HLA00427HLA07063_HLA03586HLA07064_HLA00455HLA07064_HLA02766HLA07065_HLA00430HLA07065_HLA02561HLA07065_HLA05526HLA07066_HLA00430HLA07066_HLA02561HLA07066_HLA05526HLA07067_HLA00471HLA07068_HLA00481HLA07069_HLA00430HLA07069_HLA02561HLA07069_HLA05526HLA07070_HLA00434HLA07070_HLA01326HLA07070_HLA01902HLA07070_HLA07777HLA07070_HLA07778HLA07071_HLA00433HLA07071_HLA07937HLA07071_HLA00438HLA07072_HLA00433HLA07072_HLA07937HLA07072_HLA00438HLA07073_HLA00430HLA07073_HLA02561HLA07073_HLA05526HLA07074_HLA00433HLA07074_HLA07937HLA07074_HLA00438HLA07075_HLA00427HLA07075_HLA03586HLA07076_HLA00455HLA07076_HLA02766HLA07077_HLA00471HLA07078_HLA00433HLA07078_HLA07937HLA07078_HLA00438HLA07079_HLA00433HLA07079_HLA07937HLA07079_HLA00438HLA07080_HLA00433HLA07080_HLA07937HLA07080_HLA00438HLA07081_HLA00433HLA07081_HLA07937HLA07081_HLA00438HLA07082_HLA00427HLA07082_HLA03586HLA07083_HLA00454HLA07108_HLA00427HLA07108_HLA03586HLA07109_HLA00427HLA07109_HLA03586HLA07110_HLA00447HLA07110_HLA00448HLA07111_HLA00427HLA07111_HLA03586HLA07112_HLA00478HLA07113_HLA00475HLA07114_HLA00455HLA07114_HLA02766HLA07115_HLA00481HLA07116_HLA00405HLA07117_HLA00405HLA07118_HLA00413HLA07119_HLA00413HLA07120_HLA00420HLA07120_HLA01328HLA07120_HLA03572HLA07120_HLA08080HLA07121_HLA00401HLA07122_HLA01856HLA07123_HLA00455HLA07123_HLA02766HLA07124_HLA00413HLA07125_HLA00462HLA07126_HLA00420HLA07126_HLA01328HLA07126_HLA03572HLA07126_HLA08080HLA07127_HLA00420HLA07127_HLA01328HLA07127_HLA03572HLA07127_HLA08080HLA07128_HLA00462HLA07129_HLA00462HLA07130_HLA00434HLA07130_HLA01326HLA07130_HLA01902HLA07130_HLA07777HLA07130_HLA07778HLA07131_HLA00430HLA07131_HLA02561HLA07131_HLA05526HLA07132_HLA00433HLA07132_HLA07937HLA07132_HLA00438HLA07133_HLA00434HLA07133_HLA01326HLA07133_HLA01902HLA07133_HLA07777HLA07133_HLA07778HLA07134_HLA00427HLA07134_HLA03586HLA07135_HLA00427HLA07135_HLA03586HLA07136_HLA00475HLA07137_HLA00454HLA07138_HLA00420HLA07138_HLA01328HLA07138_HLA03572HLA07138_HLA08080HLA07139_HLA00467HLA07140_HLA00410HLA07140_HLA05731HLA07141_HLA00462HLA07142_HLA00420HLA07142_HLA01328HLA07142_HLA03572HLA07142_HLA08080HLA07182_HLA00433HLA07182_HLA07937HLA07182_HLA00438HLA07213_HLA00401HLA07214_HLA00401HLA07215_HLA00434HLA07215_HLA01326HLA07215_HLA01902HLA07215_HLA07777HLA07215_HLA07778HLA07216_HLA00430HLA07216_HLA02561HLA07216_HLA05526HLA07217_HLA00433HLA07217_HLA07937HLA07217_HLA00438HLA07218_HLA00433HLA07218_HLA07937HLA07218_HLA00438HLA07219_HLA00434HLA07219_HLA01326HLA07219_HLA01902HLA07219_HLA07777HLA07219_HLA07778HLA07220_HLA00434HLA07220_HLA01326HLA07220_HLA01902HLA07220_HLA07777HLA07220_HLA07778HLA07221_HLA00434HLA07221_HLA01326HLA07221_HLA01902HLA07221_HLA07777HLA07221_HLA07778HLA07222_HLA00427HLA07222_HLA03586HLA07223_HLA00454HLA07224_HLA00427HLA07224_HLA03586HLA07225_HLA00427HLA07225_HLA03586HLA07226_HLA00427HLA07226_HLA03586HLA07227_HLA00427HLA07227_HLA03586HLA07228_HLA00427HLA07228_HLA03586HLA07229_HLA00475HLA07230_HLA00454HLA07230_HLA02766HLA07231_HLA00455HLA07231_HLA02766HLA07232_HLA00454HLA07233_HLA00481HLA07234_HLA00476HLA07235_HLA00411HLA07236_HLA00405HLA07237_HLA00405HLA07238_HLA00413HLA07239_HLA00415HLA07240_HLA00413HLA07241_HLA00413HLA07242_HLA00420HLA07242_HLA01328HLA07242_HLA03572HLA07242_HLA08080HLA07243_HLA00420HLA07243_HLA01328HLA07243_HLA03572HLA07243_HLA08080HLA07244_HLA00420HLA07244_HLA01328HLA07244_HLA03572HLA07244_HLA08080HLA07245_HLA00420HLA07245_HLA01328HLA07245_HLA03572HLA07245_HLA08080HLA07246_HLA00413HLA07272_HLA00436HLA07273_HLA00446HLA07274_HLA00462HLA07315_HLA00413HLA07316_HLA00433HLA07316_HLA07937HLA07316_HLA00438HLA07317_HLA00475HLA07318_HLA00455HLA07318_HLA02766HLA07320_HLA00434HLA07320_HLA01326HLA07320_HLA01902HLA07320_HLA07777HLA07320_HLA07778HLA07345_HLA00446HLA07348_HLA00413HLA07349_HLA00401HLA07355_HLA00410HLA07355_HLA05731HLA07357_HLA00430HLA07357_HLA02561HLA07358_HLA00427HLA07358_HLA03586HLA07360_HLA00405HLA07363_HLA03680HLA07373_HLA00434HLA07373_HLA01326HLA07373_HLA01902HLA07373_HLA07777HLA07373_HLA07778HLA07406_HLA00423HLA07416_HLA00411HLA07474_HLA00434HLA07474_HLA01326HLA07474_HLA01902HLA07474_HLA07777HLA07474_HLA07778HLA07475_HLA00401HLA07476_HLA00401HLA07477_HLA00433HLA07477_HLA07937HLA07477_HLA00438HLA07478_HLA00430HLA07478_HLA02561HLA07478_HLA05526HLA07479_HLA00430HLA07479_HLA02561HLA07479_HLA05526HLA07480_HLA00430HLA07480_HLA02561HLA07480_HLA05526HLA07481_HLA00433HLA07481_HLA07937HLA07481_HLA00438HLA07482_HLA00433HLA07482_HLA07937HLA07482_HLA00438HLA07483_HLA00433HLA07483_HLA07937HLA07483_HLA00438HLA07484_HLA00434HLA07484_HLA01326HLA07484_HLA01902HLA07484_HLA07777HLA07484_HLA07778HLA07485_HLA00434HLA07485_HLA01326HLA07485_HLA01902HLA07485_HLA07777HLA07485_HLA07778HLA07486_HLA00433HLA07486_HLA07937HLA07486_HLA00438HLA07487_HLA00427HLA07487_HLA03586HLA07488_HLA00427HLA07488_HLA03586HLA07489_HLA00448HLA07490_HLA00454HLA07491_HLA00455HLA07491_HLA02766HLA07492_HLA00430HLA07492_HLA02561HLA07492_HLA05526HLA07493_HLA00405HLA07494_HLA00467HLA07495_HLA00413HLA07496_HLA00411HLA07497_HLA00411HLA07498_HLA00414HLA07499_HLA00420HLA07499_HLA01328HLA07499_HLA03572HLA07499_HLA08080HLA07500_HLA00420HLA07500_HLA01328HLA07500_HLA03572HLA07500_HLA08080HLA07501_HLA00420HLA07501_HLA01328HLA07501_HLA03572HLA07501_HLA08080HLA07502_HLA00420HLA07502_HLA01328HLA07502_HLA03572HLA07502_HLA08080HLA07521_HLA00448HLA07526_HLA00411HLA07527_HLA00464HLA07528_HLA00401HLA07529_HLA00420HLA07529_HLA01328HLA07529_HLA03572HLA07529_HLA08080HLA07530_HLA00445HLA07531_HLA00445HLA07537_HLA00413HLA07540_HLA00462HLA07541_HLA00462HLA07555_HLA00455HLA07555_HLA02766HLA07556_HLA00401HLA07729_HLA00401HLA07730_HLA00410HLA07730_HLA05731HLA07731_HLA00434HLA07731_HLA01326HLA07731_HLA01902HLA07731_HLA07777HLA07731_HLA07778HLA07733_HLA00430HLA07733_HLA02561HLA07733_HLA05526HLA07734_HLA00434HLA07734_HLA01326HLA07734_HLA01902HLA07734_HLA07777HLA07734_HLA07778HLA07735_HLA00433HLA07735_HLA07937HLA07735_HLA00438HLA07736_HLA00433HLA07736_HLA07937HLA07736_HLA00438HLA07737_HLA00434HLA07737_HLA01326HLA07737_HLA01902HLA07737_HLA07777HLA07737_HLA07778HLA07738_HLA00434HLA07738_HLA01326HLA07738_HLA01902HLA07738_HLA07777HLA07738_HLA07778HLA07739_HLA00434HLA07739_HLA01326HLA07739_HLA01902HLA07739_HLA07777HLA07739_HLA07778HLA07740_HLA00430HLA07740_HLA02561HLA07740_HLA05526HLA07741_HLA00455HLA07741_HLA02766HLA07742_HLA00445HLA07743_HLA00445HLA07744_HLA00475HLA07745_HLA00454HLA07755_HLA00420HLA07755_HLA01328HLA07755_HLA03572HLA07755_HLA08080HLA07756_HLA00433HLA07756_HLA07937HLA07760_HLA00467HLA07763_HLA00413HLA07782_HLA00454HLA07783_HLA00454HLA07784_HLA00454HLA07785_HLA00454HLA07786_HLA00455HLA07786_HLA02766HLA07787_HLA00467HLA07788_HLA00471HLA07789_HLA00467HLA07790_HLA00467HLA07791_HLA00467HLA07804_HLA00462HLA07810_HLA00455HLA07810_HLA02766HLA07815_HLA00430HLA07815_HLA02561HLA07822_HLA00433HLA07822_HLA07937HLA07822_HLA00438HLA07824_HLA00464HLA07825_HLA00462HLA07826_HLA00430HLA07826_HLA02561HLA07826_HLA05526HLA07827_HLA00430HLA07827_HLA02561HLA07827_HLA05526HLA07828_HLA00434HLA07828_HLA01326HLA07828_HLA01902HLA07828_HLA07777HLA07828_HLA07778HLA07829_HLA00433HLA07829_HLA07937HLA07829_HLA00438HLA07830_HLA00430HLA07830_HLA02561HLA07830_HLA05526HLA07831_HLA00430HLA07831_HLA02561HLA07831_HLA05526HLA07832_HLA00430HLA07832_HLA02561HLA07832_HLA05526HLA07833_HLA00430HLA07833_HLA02561HLA07833_HLA05526HLA07834_HLA00430HLA07834_HLA02561HLA07834_HLA05526HLA07835_HLA00433HLA07835_HLA07937HLA07835_HLA00438HLA07836_HLA00433HLA07836_HLA07937HLA07836_HLA00438HLA07837_HLA02943HLA07838_HLA00434HLA07838_HLA01326HLA07838_HLA01902HLA07838_HLA07777HLA07838_HLA07778HLA07839_HLA00434HLA07839_HLA01326HLA07839_HLA01902HLA07839_HLA07777HLA07839_HLA07778HLA07840_HLA00434HLA07840_HLA01326HLA07840_HLA01902HLA07840_HLA07777HLA07840_HLA07778HLA07841_HLA00434HLA07841_HLA01326HLA07841_HLA01902HLA07841_HLA07777HLA07841_HLA07778HLA07842_HLA00410HLA07842_HLA05731HLA07842_HLA00434HLA07842_HLA01326HLA07842_HLA01902HLA07842_HLA07777HLA07842_HLA07778HLA07843_HLA00434HLA07843_HLA01326HLA07843_HLA01902HLA07843_HLA07777HLA07843_HLA07778HLA07844_HLA00434HLA07844_HLA01326HLA07844_HLA01902HLA07844_HLA07777HLA07844_HLA07778HLA07845_HLA00433HLA07845_HLA07937HLA07845_HLA00438HLA07846_HLA00433HLA07846_HLA07937HLA07846_HLA00438HLA07847_HLA00447HLA07848_HLA00476HLA07849_HLA00476HLA07850_HLA00476HLA07851_HLA00475HLA07852_HLA00455HLA07852_HLA02766HLA07853_HLA00455HLA07853_HLA02766HLA07854_HLA00455HLA07854_HLA02766HLA07855_HLA00455HLA07855_HLA02766HLA07856_HLA00455HLA07856_HLA02766HLA07857_HLA00481HLA07858_HLA00462HLA07859_HLA00462HLA07860_HLA00462HLA07861_HLA00464HLA07930_HLA00434HLA07930_HLA01326HLA07930_HLA01902HLA07930_HLA07777HLA07930_HLA07778HLA07940_HLA00413HLA07941_HLA00401HLA07942_HLA00401HLA07943_HLA00401HLA07944_HLA00405HLA07945_HLA00413HLA07946_HLA00413HLA07947_HLA00411HLA07948_HLA00411HLA07949_HLA00411HLA07950_HLA00411HLA07951_HLA00413HLA07952_HLA00413HLA07953_HLA00413HLA07954_HLA00411HLA07955_HLA00413HLA07956_HLA00413HLA07957_HLA00413HLA07965_HLA02120HLA07969_HLA00420HLA07969_HLA01328HLA07969_HLA03572HLA07969_HLA08080HLA07970_HLA00420HLA07970_HLA01328HLA07970_HLA03572HLA07970_HLA08080HLA07971_HLA00420HLA07971_HLA01328HLA07971_HLA03572HLA07971_HLA08080HLA07972_HLA00420HLA07972_HLA01328HLA07972_HLA03572HLA07972_HLA08080HLA07973_HLA00420HLA07973_HLA01328HLA07973_HLA03572HLA07973_HLA08080HLA07974_HLA00420HLA07974_HLA01328HLA07974_HLA03572HLA07974_HLA08080HLA07975_HLA00420HLA07975_HLA01328HLA07975_HLA03572HLA07975_HLA08080HLA07976_HLA00427HLA07976_HLA03586HLA07977_HLA00427HLA07977_HLA03586HLA07978_HLA00427HLA07978_HLA03586HLA07979_HLA00427HLA07979_HLA03586HLA07980_HLA00427HLA07980_HLA03586HLA07981_HLA00427HLA07981_HLA03586HLA08022_HLA00420HLA08022_HLA01328HLA08022_HLA03572HLA08022_HLA08080HLA08088_HLA00446HLA08117_HLA00475HLA08118_HLA00405HLA08119_HLA00420HLA08119_HLA01328HLA08119_HLA03572HLA08119_HLA08080HLA08124_HLA00434HLA08124_HLA01326HLA08124_HLA01902HLA08124_HLA07777HLA08124_HLA07778HLA08145_HLA00401HLA08146_HLA00401HLA08147_HLA00433HLA08147_HLA07937HLA08147_HLA00438HLA08148_HLA00430HLA08148_HLA02561HLA08148_HLA05526HLA08149_HLA00430HLA08149_HLA02561HLA08149_HLA05526HLA08150_HLA00433HLA08150_HLA07937HLA08150_HLA00438HLA08151_HLA00433HLA08151_HLA07937HLA08151_HLA00438HLA08152_HLA00433HLA08152_HLA07937HLA08152_HLA00438HLA08153_HLA00433HLA08153_HLA07937HLA08153_HLA00438HLA08153_HLA01720HLA08154_HLA00430HLA08154_HLA02561HLA08154_HLA05526HLA08155_HLA00447HLA08156_HLA00427HLA08156_HLA03586HLA08157_HLA00445HLA08158_HLA00445HLA08159_HLA00445HLA08160_HLA00454HLA08161_HLA00475HLA08162_HLA00475HLA08163_HLA00475HLA08164_HLA00481HLA08165_HLA00405HLA08166_HLA00413HLA08167_HLA00413HLA08168_HLA00413HLA08169_HLA02881HLA08170_HLA00471HLA08171_HLA00420HLA08171_HLA01328HLA08171_HLA03572HLA08171_HLA08080HLA08172_HLA00420HLA08172_HLA01328HLA08172_HLA03572HLA08172_HLA08080HLA08173_HLA00420HLA08173_HLA01328HLA08173_HLA03572HLA08173_HLA08080HLA08174_HLA00420HLA08174_HLA01328HLA08174_HLA03572HLA08174_HLA08080HLA08175_HLA00411HLA08176_HLA00413HLA08177_HLA00401HLA08178_HLA00401HLA08179_HLA00434HLA08179_HLA01326HLA08179_HLA01902HLA08179_HLA07777HLA08179_HLA07778HLA08180_HLA00434HLA08180_HLA01326HLA08180_HLA01902HLA08180_HLA07777HLA08180_HLA07778HLA08181_HLA00430HLA08181_HLA02561HLA08181_HLA05526HLA08182_HLA00430HLA08182_HLA02561HLA08182_HLA05526HLA08183_HLA00436HLA08184_HLA00436HLA08185_HLA00433HLA08185_HLA07937HLA08185_HLA00438HLA08186_HLA00433HLA08186_HLA07937HLA08186_HLA00438HLA08187_HLA00433HLA08187_HLA07937HLA08187_HLA00438HLA08188_HLA00433HLA08188_HLA07937HLA08188_HLA00438HLA08189_HLA00433HLA08189_HLA07937HLA08189_HLA00438HLA08190_HLA00434HLA08190_HLA01326HLA08190_HLA01902HLA08190_HLA07777HLA08190_HLA07778HLA08191_HLA00434HLA08191_HLA01326HLA08191_HLA01902HLA08191_HLA07777HLA08191_HLA07778HLA08192_HLA00434HLA08192_HLA01326HLA08192_HLA01902HLA08192_HLA07777HLA08192_HLA07778HLA08193_HLA00434HLA08193_HLA01326HLA08193_HLA01902HLA08193_HLA07777HLA08193_HLA07778HLA08194_HLA00434HLA08194_HLA01326HLA08194_HLA01902HLA08194_HLA07777HLA08194_HLA07778HLA08195_HLA00434HLA08195_HLA01326HLA08195_HLA01902HLA08195_HLA07777HLA08195_HLA07778HLA08196_HLA00434HLA08196_HLA01326HLA08196_HLA01902HLA08196_HLA07777HLA08196_HLA07778HLA08197_HLA00433HLA08197_HLA07937HLA08197_HLA00438HLA08198_HLA00427HLA08198_HLA03586HLA08199_HLA00427HLA08199_HLA03586HLA08200_HLA00427HLA08200_HLA03586HLA08201_HLA00446HLA08201_HLA03975HLA08202_HLA00455HLA08202_HLA02766HLA08203_HLA00475HLA08204_HLA00475HLA08205_HLA00455HLA08205_HLA02766HLA08206_HLA00413HLA08207_HLA00481HLA08208_HLA00481HLA08209_HLA00405HLA08210_HLA00405HLA08211_HLA00405HLA08212_HLA00405HLA08213_HLA00405HLA08214_HLA00411HLA08215_HLA00411HLA08216_HLA00413HLA08217_HLA00413HLA08218_HLA00455HLA08218_HLA02766HLA08219_HLA00462HLA08220_HLA00462HLA08221_HLA00420HLA08221_HLA01328HLA08221_HLA03572HLA08221_HLA08080HLA08222_HLA00420HLA08222_HLA01328HLA08222_HLA03572HLA08222_HLA08080HLA08223_HLA00420HLA08223_HLA01328HLA08223_HLA03572HLA08223_HLA08080HLA08224_HLA00420HLA08224_HLA01328HLA08224_HLA03572HLA08224_HLA08080HLA08225_HLA00420HLA08225_HLA01328HLA08225_HLA03572HLA08225_HLA08080HLA08226_HLA00420HLA08226_HLA01328HLA08226_HLA03572HLA08226_HLA08080HLA08227_HLA00420HLA08227_HLA01328HLA08227_HLA03572HLA08227_HLA08080HLA08304_HLA00462HLA08307_HLA00401HLA08399_HLA00454HLA08400_HLA00445HLA08402_HLA00434HLA08402_HLA01326HLA08402_HLA01902HLA08402_HLA07777HLA08402_HLA07778HLA08418_HLA00434HLA08418_HLA01326HLA08418_HLA01902HLA08418_HLA07777HLA08418_HLA07778HLA08419_HLA00413HLA08421_HLA00454HLA08426_HLA00454HLA08427_HLA00448HLA08428_HLA00462HLA08440_HLA00401HLA08441_HLA00420HLA08441_HLA01328HLA08441_HLA03572HLA08441_HLA08080HLA08442_HLA00433HLA08442_HLA07937HLA08442_HLA00438HLA08473_HLA00430HLA08473_HLA02561HLA08473_HLA05526HLA08474_HLA00433HLA08474_HLA07937HLA08474_HLA00438HLA08475_HLA00427HLA08475_HLA03586HLA08476_HLA00471HLA08477_HLA00411HLA08478_HLA00433HLA08478_HLA07937HLA08478_HLA00438HLA08526_HLA00433HLA08526_HLA07937HLA08526_HLA00438HLA08527_HLA00433HLA08527_HLA07937HLA08527_HLA00438HLA08528_HLA00434HLA08528_HLA01326HLA08528_HLA01902HLA08528_HLA07777HLA08528_HLA07778HLA08529_HLA00433HLA08529_HLA07937HLA08529_HLA00434HLA08529_HLA01326HLA08529_HLA01902HLA08529_HLA07777HLA08529_HLA07778HLA08529_HLA00438HLA08530_HLA00413HLA08531_HLA00481HLA08532_HLA00427HLA08532_HLA03586HLA08533_HLA00405HLA08534_HLA00467HLA08535_HLA00455HLA08535_HLA02766HLA08536_HLA00413HLA08537_HLA00415HLA08538_HLA00411HLA08539_HLA00414HLA08540_HLA00410HLA08540_HLA05731HLA08541_HLA00462HLA08542_HLA00420HLA08542_HLA01328HLA08542_HLA03572HLA08542_HLA08080HLA08543_HLA00420HLA08543_HLA01328HLA08543_HLA03572HLA08543_HLA08080HLA08544_HLA00420HLA08544_HLA01328HLA08544_HLA03572HLA08544_HLA08080HLA08545_HLA00413HLA08688_HLA00434HLA08688_HLA01326HLA08688_HLA01902HLA08688_HLA07777HLA08688_HLA07778HLA08689_HLA00436HLA08690_HLA00483HLA08691_HLA00434HLA08691_HLA01326HLA08691_HLA01902HLA08691_HLA07777HLA08691_HLA07778HLA08692_HLA00434HLA08692_HLA01326HLA08692_HLA01902HLA08692_HLA07777HLA08692_HLA07778HLA08693_HLA00430HLA08693_HLA02561HLA08693_HLA05526HLA08694_HLA00467HLA08695_HLA00430HLA08695_HLA02561HLA08695_HLA05526HLA08696_HLA00430HLA08696_HLA02561HLA08696_HLA05526HLA08697_HLA00430HLA08697_HLA02561HLA08697_HLA05526HLA08698_HLA00430HLA08698_HLA02561HLA08698_HLA05526HLA08699_HLA00430HLA08699_HLA02561HLA08699_HLA05526HLA08700_HLA00430HLA08700_HLA02561HLA08700_HLA05526HLA08701_HLA00430HLA08701_HLA02561HLA08702_HLA00430HLA08702_HLA02561HLA08702_HLA05526HLA08703_HLA00434HLA08703_HLA01326HLA08703_HLA01902HLA08703_HLA07777HLA08703_HLA07778HLA08704_HLA00433HLA08704_HLA07937HLA08704_HLA00438HLA08705_HLA00433HLA08705_HLA07937HLA08705_HLA00438HLA08706_HLA00433HLA08706_HLA07937HLA08706_HLA00438HLA08707_HLA00433HLA08707_HLA07937HLA08707_HLA00438HLA08708_HLA00433HLA08708_HLA07937HLA08708_HLA00438HLA08709_HLA00433HLA08709_HLA07937HLA08709_HLA00438HLA08710_HLA00433HLA08710_HLA07937HLA08710_HLA00438HLA08711_HLA00433HLA08711_HLA07937HLA08711_HLA00438HLA08712_HLA00433HLA08712_HLA07937HLA08712_HLA00438HLA08713_HLA00433HLA08713_HLA07937HLA08713_HLA00438HLA08714_HLA00434HLA08714_HLA01326HLA08714_HLA01902HLA08714_HLA07777HLA08714_HLA07778HLA08715_HLA00434HLA08715_HLA01326HLA08715_HLA01902HLA08715_HLA07777HLA08715_HLA07778HLA08716_HLA00434HLA08716_HLA01326HLA08716_HLA01902HLA08716_HLA07777HLA08716_HLA07778HLA08717_HLA00434HLA08717_HLA01326HLA08717_HLA01902HLA08717_HLA07777HLA08717_HLA07778HLA08718_HLA00434HLA08718_HLA01326HLA08718_HLA01902HLA08718_HLA07777HLA08718_HLA07778HLA08719_HLA00434HLA08719_HLA01326HLA08719_HLA01902HLA08719_HLA07777HLA08719_HLA07778HLA08720_HLA00434HLA08720_HLA01326HLA08720_HLA01902HLA08720_HLA07777HLA08720_HLA07778HLA08721_HLA00434HLA08721_HLA01326HLA08721_HLA01902HLA08721_HLA07777HLA08721_HLA07778HLA08722_HLA00434HLA08722_HLA01326HLA08722_HLA01902HLA08722_HLA07777HLA08722_HLA07778HLA08723_HLA00434HLA08723_HLA01326HLA08723_HLA01902HLA08723_HLA07777HLA08723_HLA07778HLA08724_HLA00434HLA08724_HLA01326HLA08724_HLA01902HLA08724_HLA07777HLA08724_HLA07778HLA08725_HLA00434HLA08725_HLA01326HLA08725_HLA01902HLA08725_HLA07777HLA08725_HLA07778HLA08726_HLA00433HLA08726_HLA07937HLA08726_HLA00438HLA08727_HLA00434HLA08727_HLA01326HLA08727_HLA01902HLA08727_HLA07777HLA08727_HLA07778HLA08728_HLA00446HLA08729_HLA00446HLA08730_HLA00427HLA08730_HLA03586HLA08731_HLA00446HLA08732_HLA00427HLA08732_HLA03586HLA08733_HLA00427HLA08733_HLA03586HLA08734_HLA00427HLA08734_HLA03586HLA08735_HLA00427HLA08735_HLA03586HLA08736_HLA00427HLA08736_HLA03586HLA08737_HLA00427HLA08737_HLA03586HLA08738_HLA00446HLA08739_HLA00446HLA08740_HLA00448HLA08741_HLA00445HLA08742_HLA00455HLA08742_HLA02766HLA08743_HLA00475HLA08744_HLA00454HLA08745_HLA00455HLA08745_HLA02766HLA08746_HLA00455HLA08746_HLA02766HLA08747_HLA00455HLA08747_HLA02766HLA08748_HLA00455HLA08748_HLA02766HLA08749_HLA00427HLA08749_HLA03586HLA08750_HLA00481HLA08751_HLA00455HLA08751_HLA02766HLA08752_HLA00455HLA08752_HLA02766HLA08753_HLA00446HLA08754_HLA00405HLA08755_HLA00405HLA08756_HLA00405HLA08757_HLA00467HLA08758_HLA00467HLA08759_HLA00467HLA08760_HLA00467HLA08761_HLA00467HLA08762_HLA01889HLA08763_HLA00467HLA08764_HLA00413HLA08765_HLA00413HLA08766_HLA00413HLA08767_HLA00413HLA08768_HLA00411HLA08808_HLA01889HLA08811_HLA00475HLA08812_HLA00411HLA08813_HLA00411HLA08813_HLA01412HLA08814_HLA01412HLA08815_HLA00413HLA08816_HLA00413HLA08817_HLA00413HLA08818_HLA00411HLA08819_HLA00462HLA08820_HLA00462HLA08821_HLA00462HLA08822_HLA00420HLA08822_HLA01328HLA08822_HLA03572HLA08822_HLA08080HLA08823_HLA00420HLA08823_HLA01328HLA08823_HLA03572HLA08823_HLA08080HLA08824_HLA00420HLA08824_HLA01328HLA08824_HLA03572HLA08824_HLA08080HLA08825_HLA00420HLA08825_HLA01328HLA08825_HLA03572HLA08825_HLA08080HLA08826_HLA00420HLA08826_HLA01328HLA08826_HLA03572HLA08826_HLA08080HLA08827_HLA00420HLA08827_HLA01328HLA08827_HLA03572HLA08827_HLA08080HLA08828_HLA00420HLA08828_HLA01328HLA08828_HLA03572HLA08828_HLA08080HLA08829_HLA00420HLA08829_HLA01328HLA08829_HLA03572HLA08829_HLA08080HLA08830_HLA00420HLA08830_HLA01328HLA08830_HLA03572HLA08830_HLA08080HLA08831_HLA00420HLA08831_HLA01328HLA08831_HLA03572HLA08831_HLA08080HLA08832_HLA00420HLA08832_HLA01328HLA08832_HLA03572HLA08832_HLA08080HLA08833_HLA00433HLA08833_HLA07937HLA08833_HLA00438HLA08885_HLA00401HLA08892_HLA00475HLA08893_HLA00455HLA08893_HLA02766HLA08897_HLA00433HLA08897_HLA07937HLA08897_HLA00434HLA08897_HLA01326HLA08897_HLA01902HLA08897_HLA07777HLA08897_HLA07778HLA08897_HLA00438HLA08932_HLA00478HLA08954_HLA00413HLA09012_HLA00401HLA09013_HLA00433HLA09013_HLA07937HLA09013_HLA00438HLA09014_HLA00430HLA09014_HLA02561HLA09014_HLA05526HLA09015_HLA00430HLA09015_HLA02561HLA09015_HLA05526HLA09016_HLA00430HLA09016_HLA02561HLA09016_HLA05526HLA09017_HLA00430HLA09017_HLA02561HLA09017_HLA05526HLA09018_HLA00433HLA09018_HLA07937HLA09018_HLA00438HLA09019_HLA00433HLA09019_HLA07937HLA09019_HLA00438HLA09020_HLA00433HLA09020_HLA07937HLA09020_HLA00438HLA09021_HLA00433HLA09021_HLA07937HLA09021_HLA00438HLA09022_HLA00433HLA09022_HLA07937HLA09022_HLA00438HLA09023_HLA00446HLA09024_HLA00427HLA09024_HLA03586HLA09025_HLA00427HLA09025_HLA03586HLA09026_HLA00446HLA09027_HLA00475HLA09028_HLA00475HLA09029_HLA00455HLA09029_HLA02766HLA09030_HLA00481HLA09031_HLA00481HLA09032_HLA00481HLA09033_HLA00481HLA09034_HLA00427HLA09034_HLA03586HLA09035_HLA00405HLA09036_HLA00471HLA09037_HLA00471HLA09038_HLA00413HLA09039_HLA00414HLA09040_HLA00413HLA09041_HLA00411HLA09042_HLA00413HLA09043_HLA00420HLA09043_HLA01328HLA09043_HLA03572HLA09043_HLA08080HLA09044_HLA00420HLA09044_HLA01328HLA09044_HLA03572HLA09044_HLA08080HLA09045_HLA00420HLA09045_HLA01328HLA09045_HLA03572HLA09045_HLA08080HLA09046_HLA00420HLA09046_HLA01328HLA09046_HLA03572HLA09046_HLA08080HLA09047_HLA00420HLA09047_HLA01328HLA09047_HLA03572HLA09047_HLA08080HLA09048_HLA00420HLA09048_HLA01328HLA09048_HLA03572HLA09048_HLA08080HLA09049_HLA00420HLA09049_HLA01328HLA09049_HLA03572HLA09049_HLA08080HLA09050_HLA00420HLA09050_HLA01328HLA09050_HLA03572HLA09050_HLA08080HLA09051_HLA00446HLA09086_HLA00455HLA09086_HLA02766HLA09111_HLA00401HLA09115_HLA00475HLA09133_HLA00427HLA09133_HLA03586HLA09136_HLA00433HLA09136_HLA07937HLA09136_HLA00438HLA09166_HLA00446HLA09176_HLA00420HLA09176_HLA01328HLA09176_HLA03572HLA09176_HLA08080HLA09177_HLA00434HLA09177_HLA01326HLA09177_HLA01902HLA09177_HLA07777HLA09177_HLA07778HLA09178_HLA00433HLA09178_HLA07937HLA09178_HLA00438HLA09179_HLA00430HLA09179_HLA02561HLA09179_HLA05526HLA09180_HLA00430HLA09180_HLA02561HLA09180_HLA05526HLA09181_HLA00430HLA09181_HLA02561HLA09181_HLA05526HLA09182_HLA00430HLA09182_HLA02561HLA09182_HLA05526HLA09183_HLA00436HLA09184_HLA00433HLA09184_HLA07937HLA09184_HLA00438HLA09185_HLA00433HLA09185_HLA07937HLA09185_HLA00438HLA09186_HLA00434HLA09186_HLA01326HLA09186_HLA01902HLA09186_HLA07777HLA09186_HLA07778HLA09187_HLA00434HLA09187_HLA01326HLA09187_HLA01902HLA09187_HLA07777HLA09187_HLA07778HLA09188_HLA00434HLA09188_HLA01326HLA09188_HLA01902HLA09188_HLA07777HLA09188_HLA07778HLA09189_HLA01843HLA09190_HLA00427HLA09190_HLA03586HLA09191_HLA00427HLA09191_HLA03586HLA09192_HLA00427HLA09192_HLA03586HLA09193_HLA00446HLA09194_HLA00446HLA09195_HLA00475HLA09196_HLA00455HLA09196_HLA02766HLA09197_HLA00413HLA09198_HLA00411HLA09199_HLA00411HLA09200_HLA00411HLA09201_HLA00411HLA09202_HLA00405HLA09203_HLA00462HLA09204_HLA00462HLA09205_HLA00420HLA09205_HLA01328HLA09205_HLA03572HLA09205_HLA08080HLA09206_HLA00420HLA09206_HLA01328HLA09206_HLA03572HLA09206_HLA08080HLA09207_HLA00420HLA09207_HLA01328HLA09207_HLA03572HLA09207_HLA08080HLA09299_HLA00454HLA09300_HLA00401HLA09330_HLA00410HLA09330_HLA05731HLA09451_HLA00434HLA09451_HLA01326HLA09451_HLA01902HLA09451_HLA07777HLA09451_HLA07778HLA09473_HLA00430HLA09473_HLA02561HLA09515_HLA00430HLA09515_HLA02561HLA09518_HLA00427HLA09518_HLA03586HLA09596_HLA00401HLA09597_HLA00413HLA09598_HLA00434HLA09598_HLA01326HLA09598_HLA01902HLA09598_HLA07777HLA09598_HLA07778HLA09599_HLA00430HLA09599_HLA02561HLA09599_HLA05526HLA09600_HLA00483HLA09601_HLA00430HLA09601_HLA02561HLA09601_HLA05526HLA09602_HLA00433HLA09602_HLA07937HLA09602_HLA00438HLA09603_HLA00433HLA09603_HLA07937HLA09603_HLA00438HLA09604_HLA00434HLA09604_HLA01326HLA09604_HLA01902HLA09604_HLA07777HLA09604_HLA07778HLA09605_HLA00434HLA09605_HLA01326HLA09605_HLA01902HLA09605_HLA07777HLA09605_HLA07778HLA09606_HLA00433HLA09606_HLA07937HLA09606_HLA00438HLA09607_HLA00433HLA09607_HLA07937HLA09607_HLA00438HLA09608_HLA00434HLA09608_HLA01326HLA09608_HLA01902HLA09608_HLA07777HLA09608_HLA07778HLA09609_HLA00427HLA09609_HLA03586HLA09610_HLA00445HLA09611_HLA00455HLA09611_HLA02766HLA09612_HLA00475HLA09613_HLA00455HLA09613_HLA02766HLA09614_HLA00455HLA09614_HLA02766HLA09615_HLA00410HLA09615_HLA05731HLA09616_HLA00405HLA09617_HLA00423HLA09618_HLA00467HLA09619_HLA00467HLA09620_HLA00467HLA09621_HLA00471HLA09622_HLA00471HLA09623_HLA00467HLA09624_HLA00411HLA09625_HLA00413HLA09626_HLA00410HLA09626_HLA05731HLA09627_HLA00471HLA09628_HLA00420HLA09628_HLA01328HLA09628_HLA03572HLA09628_HLA08080HLA09629_HLA00420HLA09629_HLA01328HLA09629_HLA03572HLA09629_HLA08080HLA09630_HLA00420HLA09630_HLA01328HLA09630_HLA03572HLA09630_HLA08080HLA09631_HLA00420HLA09631_HLA01328HLA09631_HLA03572HLA09631_HLA08080HLA09632_HLA00420HLA09632_HLA01328HLA09632_HLA03572HLA09632_HLA08080HLA09669_HLA00401HLA09671_HLA00411HLA09679_HLA00427HLA09679_HLA03586HLA09689_HLA00434HLA09689_HLA01326HLA09689_HLA01902HLA09689_HLA07777HLA09689_HLA07778HLA09716_HLA00423HLA09717_HLA00402HLA09725_HLA00430HLA09725_HLA02561HLA09725_HLA05526HLA09726_HLA00411HLA09727_HLA00462HLA09728_HLA00420HLA09728_HLA01328HLA09728_HLA03572HLA09728_HLA08080HLA09820_HLA00462HLA09822_HLA00475HLA09831_HLA02943HLA09834_HLA00445HLA00934HLA00936HLA00937HLA05913HLA00938_HLA00936HLA00938_HLA00937HLA00938_HLA05913HLA01339_HLA00937HLA01339_HLA05913HLA09519_HLA00936HLA01096HLA02271HLA02274HLA02266HLA02269HLA01755HLA02265HLA02279HLA02267HLA02276HLA02268HLA02272HLA00939HLA02288HLA02281HLA02282HLA03588HLA00940HLA02285HLA00941HLA07532HLA00943HLA00944HLA00946HLA02284HLA02972HLA04419HLA07536HLA00948HLA06452HLA00949HLA00951HLA00952HLA02286HLA00942_HLA00939HLA00942_HLA02288HLA00942_HLA02281HLA00942_HLA02282HLA00942_HLA03588HLA00942_HLA00944HLA00945_HLA00940HLA00945_HLA02285HLA00945_HLA00941HLA00945_HLA07532HLA00947_HLA00939HLA00947_HLA02288HLA00947_HLA02281HLA00947_HLA02282HLA00947_HLA03588HLA00950_HLA00944HLA00950_HLA00949HLA02954_HLA00939HLA02954_HLA02288HLA02954_HLA02281HLA02954_HLA02282HLA02954_HLA03588HLA02969_HLA00940HLA02969_HLA02285HLA02973_HLA00940HLA02973_HLA02285HLA03159_HLA00940HLA03159_HLA02285HLA03192_HLA00939HLA03192_HLA02288HLA03192_HLA02281HLA03192_HLA02282HLA03192_HLA03588HLA03192_HLA00944HLA03193_HLA00949HLA03396_HLA00946HLA03397_HLA00940HLA03397_HLA02285HLA03398_HLA00946HLA03398_HLA01357HLA03399_HLA00949HLA03400_HLA01357HLA03552_HLA00940HLA03552_HLA02285HLA03553_HLA00939HLA03553_HLA02288HLA03553_HLA02281HLA03553_HLA02282HLA03553_HLA03588HLA03555_HLA00949HLA03556_HLA00940HLA03556_HLA02285HLA04000_HLA00940HLA04000_HLA02285HLA02546HLA02557HLA02548HLA02551HLA02547HLA02549HLA02556HLA02550HLA02552HLA02553_HLA02546HLA02553_HLA02557HLA02553_HLA02548HLA02554_HLA02547HLA02554_HLA02549HLA02555_HLA02552HLA02626HLA02629HLA02630HLA02632HLA02628HLA02631HLA02627HLA02654HLA02658HLA02657HLA02659HLA02656HLA02660HLA02655HLA02661HLA02664HLA02801HLA02802HLA02803 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-HLA00001HLA02169HLA01244HLA01971HLA02540HLA03131HLA03742HLA03799HLA03930HLA04425HLA04427HLA04470HLA04524HLA04558HLA04804HLA05157HLA05319HLA05326HLA05332HLA05348HLA05546HLA05662HLA05684HLA05685HLA05725HLA05726HLA05907HLA05933HLA05934HLA05968HLA05988HLA05989HLA06020HLA06097HLA06103HLA06329HLA06548HLA06563HLA03587HLA06745HLA06786HLA06790HLA06803HLA06911HLA07605HLA07674HLA07992HLA07994HLA08444HLA08461HLA08637HLA08781HLA08966HLA08968HLA09414HLA09415HLA09417HLA09537HLA09539HLA00002HLA00003HLA00004HLA01031HLA01208HLA01292HLA01496HLA01882HLA06802HLA06813HLA07351HLA07356HLA07404HLA07596HLA07597HLA07776HLA07806HLA07807HLA07989HLA07991HLA07993HLA08248HLA08557HLA08445HLA08446HLA08447HLA08460HLA08486HLA02057HLA02108HLA08636HLA08638HLA08639HLA08895HLA08920HLA08965HLA08967HLA09151HLA09339HLA09416HLA02110HLA09466HLA09506HLA09507HLA09538HLA09799HLA09800HLA09801HLA09802HLA09803HLA02152HLA02183HLA02310HLA02373HLA02484HLA02491HLA02537HLA02857HLA02878HLA02891HLA02895HLA02897HLA02920HLA02946HLA02985HLA03029HLA03030HLA03501HLA03522HLA03577HLA03688HLA03789HLA03831HLA03877HLA03879HLA03881HLA03882HLA03898HLA04122HLA04151HLA04137HLA04469HLA04491HLA04494HLA04525HLA04527HLA04546HLA04761HLA04773HLA04808HLA04811HLA05224HLA05321HLA05323HLA05324HLA05327HLA05329HLA05330HLA05334HLA05338HLA05344HLA05398HLA05427HLA05429HLA05432HLA07473HLA05440HLA05539HLA05630HLA05635HLA05648HLA05661HLA05670HLA05838HLA05894HLA05904HLA05906HLA05908HLA05932HLA05978HLA08640HLA05987HLA06006HLA06341HLA06531HLA06549HLA06558HLA06561HLA06569HLA06570HLA06571HLA06764HLA06765HLA06787HLA06799HLA06800HLA06801HLA00005HLA01785HLA03253HLA00006HLA00966HLA01032HLA01327HLA01332HLA01624HLA01664HLA01682HLA01893HLA02000HLA02312HLA02854HLA02908HLA02914HLA03095HLA03199HLA03218HLA03524HLA03534HLA03787HLA03790HLA03792HLA03794HLA03798HLA03883HLA03887HLA03889HLA03897HLA03943HLA04421HLA04426HLA04428HLA04431HLA04477HLA04479HLA04480HLA04482HLA04484HLA04557HLA04674HLA04807HLA04814HLA05140HLA05228HLA05230HLA05243HLA05356HLA05654HLA05668HLA05693HLA05698HLA06090HLA06347HLA06567HLA06573HLA06657HLA06661HLA06768HLA06779HLA06791HLA07283HLA07436HLA07438HLA07610HLA07615HLA07616HLA07617HLA07620HLA07753HLA07774HLA08006HLA08008HLA08014HLA08015HLA08017HLA08056HLA08128HLA08555HLA08465HLA08497HLA08651HLA08652HLA09549HLA09552HLA09686HLA09810HLA09811HLA09813HLA09814HLA09816HLA09817HLA00007HLA00008HLA01945HLA05409HLA06091HLA00009HLA00010HLA03656HLA03896HLA05980HLA06105HLA08561HLA00011HLA01956HLA01965HLA02919HLA03026HLA03290HLA04062HLA04478HLA04550HLA05640HLA07608HLA08003HLA08103HLA09324HLA00012HLA07326HLA00013HLA00014HLA00015HLA02538HLA06098HLA02541HLA02582HLA02668HLA02703HLA02707HLA02711HLA02724HLA02755HLA02776HLA02778HLA02840HLA02867HLA02896HLA02899HLA02901HLA02915HLA02935HLA02936HLA00016HLA05644HLA06102HLA06089HLA00017HLA02937HLA02953HLA02956HLA02957HLA02960HLA02961HLA02964HLA03021HLA03022HLA03076HLA00018HLA03083HLA03096HLA03118HLA03132HLA03144HLA03145HLA03162HLA03181HLA03229HLA03235HLA00019HLA03241HLA03284HLA03304HLA03305HLA03306HLA03326HLA03330HLA03346HLA03409HLA03421HLA03452HLA03475HLA03497HLA03567HLA03579HLA03580HLA03582HLA03629HLA03652HLA03653HLA00020HLA00021HLA03655HLA03657HLA03669HLA03670HLA03671HLA03672HLA03673HLA03721HLA03744HLA03774HLA03776HLA03777HLA04646HLA03784HLA03785HLA03786HLA03791HLA03795HLA03815HLA03829HLA03833HLA00022HLA00023HLA09325HLA00024HLA03880HLA03884HLA03886HLA03892HLA03893HLA03895HLA03932HLA04063HLA04064HLA04065HLA00025HLA03996HLA04018HLA04120HLA04121HLA04149HLA04152HLA04420HLA04423HLA04424HLA04430HLA04928HLA04943HLA04944HLA04945HLA04948HLA04949HLA04951HLA04952HLA04953HLA04968HLA00026HLA01260HLA00027HLA04969HLA04970HLA06780HLA04971HLA04972HLA04973HLA04975HLA04976HLA04984HLA06526HLA04985HLA04986HLA04987HLA04989HLA04990HLA04991HLA05001HLA05002HLA05003HLA05004HLA05005HLA05020HLA00028HLA03808HLA04887HLA05037HLA05038HLA05039HLA05040HLA05041HLA05042HLA05043HLA05044HLA05045HLA05046HLA04890HLA04891HLA04893HLA05098HLA05078HLA05087HLA05102HLA05104HLA05225HLA00030HLA05964HLA00031HLA05226HLA05227HLA05229HLA05231HLA05245HLA05247HLA05244HLA05307HLA05360HLA05368HLA00032HLA05373HLA05375HLA05384HLA05399HLA05420HLA05422HLA05408HLA05523HLA05532HLA05542HLA00033HLA05549HLA05556HLA05672HLA05676HLA05677HLA05687HLA05691HLA05696HLA05697HLA05801HLA00034HLA05895HLA05896HLA05897HLA05948HLA05963HLA05991HLA06008HLA06009HLA06016HLA06017HLA00035HLA06019HLA06077HLA06079HLA06080HLA06081HLA06082HLA06088HLA06092HLA06099HLA06106HLA00036HLA06108HLA06109HLA06336HLA06342HLA06346HLA06373HLA06564HLA06565HLA06566HLA06572HLA00967HLA06576HLA06663HLA06747HLA06758HLA06759HLA06760HLA06767HLA06792HLA06805HLA06821HLA06832HLA07034HLA07037HLA06895HLA06900HLA06912HLA06913HLA07104HLA07279HLA07281HLA00968HLA01033HLA07287HLA07291HLA07292HLA07324HLA07342HLA07380HLA07387HLA07430HLA07431HLA07432HLA01034HLA07433HLA07434HLA07435HLA07437HLA07607HLA07611HLA07612HLA07613HLA07614HLA07618HLA07619HLA07621HLA07622HLA07677HLA07678HLA07747HLA07765HLA07817HLA07821HLA08002HLA01035HLA01946HLA02938HLA01036HLA08005HLA08007HLA08009HLA08010HLA08011HLA08012HLA08013HLA08016HLA08018HLA08019HLA01102HLA08021HLA08081HLA08096HLA08129HLA08303HLA08468HLA08558HLA08462HLA08463HLA08464HLA01105HLA08466HLA08467HLA08493HLA08494HLA08495HLA08496HLA08498HLA08645HLA08646HLA08647HLA01109HLA08648HLA08649HLA08650HLA08883HLA08888HLA08889HLA08891HLA08896HLA08972HLA08973HLA08974HLA09079HLA09090HLA09099HLA09121HLA09123HLA09125HLA09126HLA09130HLA09163HLA01121HLA08127HLA01172HLA09164HLA09171HLA09298HLA09421HLA09422HLA09468HLA09463HLA09481HLA09494HLA01198HLA09486HLA09548HLA09550HLA09551HLA09553HLA09516HLA09644HLA09662HLA09688HLA09692HLA09693HLA09715HLA09718HLA09808HLA09809HLA09812HLA09815HLA09877HLA01218HLA01222HLA01249HLA01274HLA01324HLA01331HLA01404HLA01431HLA01478HLA01533HLA01534HLA01545HLA01562HLA01575HLA03474HLA01609HLA01610HLA01666HLA01665HLA05821HLA01699HLA01709HLA01735HLA01760HLA01778HLA01781HLA01802HLA01867HLA01903HLA01928HLA01942HLA01955HLA01972HLA02028HLA02126HLA02051HLA02081HLA07333HLA02082HLA02094HLA02105HLA05898HLA02160HLA02168HLA02194HLA02202HLA02233HLA02235HLA02248HLA02321HLA02337HLA02351HLA02374HLA02435HLA02440HLA02468HLA02476HLA02481HLA02501HLA02509HLA03980HLA02529HLA00037HLA01718HLA01960HLA00038HLA00039HLA02024HLA02576HLA02992HLA03521HLA03530HLA03543HLA03578HLA03743HLA03800HLA03872HLA03873HLA03927HLA04148HLA04422HLA05335HLA05337HLA05453HLA05665HLA05686HLA05689HLA06328HLA06345HLA06351HLA06362HLA06562HLA06746HLA06766HLA06772HLA07598HLA07602HLA08448HLA08488HLA08489HLA08492HLA08641HLA09118HLA09469HLA09543HLA09545HLA09546HLA00040HLA06756HLA07409HLA00041HLA00042HLA06087HLA08450HLA01107HLA07996HLA01251HLA01275HLA01302HLA01477HLA01646HLA05663HLA05664HLA05675HLA05680HLA05688HLA05701HLA05703HLA05704HLA05705HLA05707HLA05724HLA05730HLA05832HLA05935HLA05945HLA05990HLA06095HLA06096HLA06370HLA06550HLA01714HLA01771HLA06551HLA06559HLA06560HLA06771HLA09542HLA06753HLA06755HLA06788HLA06804HLA06881HLA06892HLA01826HLA06910HLA07038HLA07040HLA07297HLA07353HLA07405HLA07427HLA07595HLA07599HLA07600HLA01827HLA07601HLA07675HLA07676HLA07803HLA07990HLA07995HLA07997HLA07999HLA08000HLA08001HLA02109HLA08020HLA08281HLA08320HLA08449HLA08451HLA08452HLA08459HLA08487HLA08490HLA08571HLA02111HLA08642HLA08644HLA08882HLA09337HLA09418HLA09419HLA09420HLA09497HLA09514HLA09540HLA09541HLA09707HLA09804HLA09805HLA09806HLA02197HLA07998HLA02290HLA02322HLA02325HLA02369HLA02405HLA06873HLA02528HLA06005HLA02590HLA02683HLA02761HLA02779HLA02858HLA02894HLA02962HLA03002HLA03023HLA03082HLA03090HLA03100HLA03119HLA03120HLA03140HLA03188HLA03423HLA03435HLA03469HLA03518HLA03525HLA03548HLA03568HLA03654HLA03667HLA03668HLA03709HLA03710HLA03870HLA03874HLA03894HLA03914HLA03917HLA03922HLA03929HLA03931HLA04131HLA04150HLA04142HLA04490HLA04492HLA04528HLA04530HLA04559HLA04561HLA04562HLA04575HLA04578HLA04636HLA04644HLA04647HLA04795HLA04859HLA05232HLA05233HLA05314HLA05333HLA05336HLA05359HLA05436HLA05439HLA05441HLA05456HLA05462HLA05547HLA05552HLA05611HLA05628HLA05631HLA05636HLA05638HLA05643HLA05646HLA05647HLA05651HLA05653HLA00043HLA01037HLA02011HLA02025HLA02216HLA02723HLA02829HLA03124HLA03211HLA03494HLA03803HLA03899HLA03910HLA03928HLA04476HLA04529HLA04855HLA05114HLA05246HLA05318HLA05343HLA05366HLA05454HLA05540HLA05629HLA05658HLA05727HLA06044HLA06331HLA06740HLA06807HLA06851HLA07099HLA07101HLA07295HLA07429HLA07558HLA07575HLA07577HLA07672HLA07982HLA08257HLA08258HLA08260HLA08266HLA09158HLA09453HLA09523HLA09774HLA00044HLA02442HLA03247HLA09301HLA00045HLA00046HLA00047HLA01104HLA01297HLA01298HLA01310HLA01423HLA06377HLA06520HLA06527HLA06555HLA06741HLA06809HLA06797HLA07106HLA07288HLA07294HLA01547HLA07389HLA07394HLA07410HLA07548HLA07573HLA07574HLA07576HLA07578HLA07579HLA07668HLA09682HLA01556HLA07749HLA07793HLA07818HLA07983HLA08095HLA08100HLA08104HLA08109HLA08259HLA08309HLA01576HLA08481HLA08614HLA08618HLA08878HLA08930HLA08941HLA08942HLA08943HLA08944HLA09081HLA01647HLA09141HLA09327HLA09459HLA09480HLA09484HLA09496HLA09508HLA09780HLA09781HLA09782HLA09788HLA01815HLA03112HLA01829HLA01839HLA01973HLA01987HLA02045HLA02052HLA02101HLA02124HLA02386HLA03327HLA02456HLA02462HLA02530HLA02601HLA02775HLA02921HLA02975HLA03332HLA05711HLA03351HLA03353HLA03394HLA03422HLA03529HLA03532HLA03576HLA03686HLA03690HLA03750HLA03814HLA03878HLA03890HLA03918HLA04123HLA04127HLA04135HLA04147HLA04139HLA04465HLA04417HLA04724HLA04744HLA04772HLA04854HLA05116HLA05234HLA05235HLA05313HLA05322HLA05434HLA05450HLA05455HLA05458HLA05529HLA05545HLA05659HLA05678HLA05699HLA05728HLA05792HLA05796HLA05798HLA05872HLA05899HLA05900HLA05931HLA05939HLA05940HLA05985HLA06003HLA06027HLA06083HLA06110HLA06085HLA06100HLA06101HLA06104HLA06107HLA06332HLA06339HLA06344HLA06361HLA06367HLA06375HLA00048HLA03788HLA05426HLA05553HLA05823HLA06762HLA06781HLA07426HLA07594HLA08271HLA08628HLA01038HLA01039HLA03177HLA01108HLA01111HLA01210HLA01470HLA01492HLA01571HLA01757HLA01834HLA01847HLA02328HLA02349HLA08277HLA02892HLA02948HLA03165HLA03170HLA03183HLA03597HLA03691HLA04069HLA04485HLA04487HLA04489HLA05236HLA05433HLA05435HLA05449HLA05524HLA05555HLA06015HLA06084HLA06086HLA06093HLA06094HLA06350HLA08272HLA06368HLA06547HLA06577HLA06763HLA06785HLA06798HLA06811HLA06838HLA07042HLA07175HLA07398HLA07403HLA07415HLA07772HLA07986HLA07987HLA08274HLA08629HLA08953HLA09119HLA09321HLA09530HLA09794HLA00050HLA00051HLA06112HLA00052HLA01616HLA01648HLA01828HLA01997HLA02204HLA02299HLA02347HLA02353HLA02416HLA02652HLA02706HLA02869HLA03196HLA03328HLA03541HLA03740HLA03741HLA03781HLA03924HLA04068HLA04153HLA04154HLA04155HLA04156HLA04429HLA04483HLA04488HLA04493HLA04683HLA05238HLA05239HLA05248HLA05353HLA05364HLA05461HLA05669HLA05743HLA05795HLA05922HLA06114HLA06116HLA06118HLA06379HLA06538HLA06544HLA06750HLA06810HLA06886HLA06899HLA07423HLA07424HLA07425HLA07563HLA07752HLA07988HLA08004HLA08273HLA08298HLA08300HLA08633HLA08634HLA08952HLA09675HLA09795HLA09796HLA09798HLA09825HLA09878HLA00053HLA01040HLA00054HLA00055HLA00056HLA00057HLA00058HLA00059HLA04894HLA04895HLA04896HLA04897HLA04898HLA04899HLA04905HLA04862HLA04863HLA04906HLA00060HLA08627HLA04908HLA04909HLA04865HLA04926HLA04927HLA04942HLA04950HLA04954HLA04955HLA04956HLA00061HLA04957HLA04958HLA04988HLA05006HLA05007HLA05008HLA05019HLA04869HLA04870HLA04871HLA04876HLA04883HLA04885HLA05103HLA05105HLA05107HLA08585HLA05084HLA05085HLA05086HLA05088HLA00063HLA03101HLA00064HLA05110HLA05117HLA05237HLA05240HLA05249HLA05550HLA05673HLA05674HLA05679HLA05729HLA00065HLA05793HLA05797HLA05800HLA05901HLA05909HLA05910HLA06004HLA06014HLA06046HLA06064HLA06111HLA06113HLA06115HLA06117HLA06119HLA06196HLA06197HLA06202HLA06203HLA06207HLA00067HLA06208HLA06291HLA06333HLA06545HLA06546HLA06556HLA06557HLA06568HLA06744HLA06751HLA00068HLA06752HLA06793HLA06812HLA07102HLA07176HLA07323HLA07341HLA07399HLA07400HLA07417HLA00069HLA07402HLA07547HLA07588HLA07589HLA07590HLA07591HLA07592HLA07593HLA07750HLA07770HLA00070HLA07984HLA07985HLA08024HLA08025HLA08115HLA08270HLA08275HLA08276HLA08278HLA08279HLA08295HLA08554HLA08560HLA08484HLA08602HLA08625HLA08626HLA08630HLA08631HLA00969HLA05365HLA00970HLA08632HLA08635HLA08786HLA08921HLA08923HLA08935HLA08950HLA08951HLA08964HLA09078HLA01041HLA09109HLA09331HLA09458HLA09498HLA09495HLA09531HLA09532HLA09533HLA09534HLA09535HLA01042HLA09536HLA09790HLA09791HLA09792HLA09793HLA09797HLA01189HLA01171HLA01220HLA01268HLA01316HLA01317HLA01330HLA01465HLA01491HLA01549HLA01566HLA01583HLA01649HLA01674HLA01773HLA01821HLA01823HLA01872HLA01957HLA01962HLA01974HLA01988HLA02037HLA02049HLA02053HLA02107HLA02125HLA02181HLA02198HLA02237HLA02362HLA02366HLA02365HLA02401HLA02417HLA02443HLA02449HLA02466HLA02524HLA02574HLA02613HLA02704HLA02725HLA02774HLA02777HLA02788HLA02860HLA02861HLA02862HLA09485HLA02863HLA02877HLA02958HLA02963HLA02984HLA03000HLA03031HLA03032HLA03117HLA03154HLA03201HLA03251HLA03331HLA03333HLA03347HLA03352HLA03395HLA03457HLA03466HLA03496HLA03535HLA03540HLA03569HLA03593HLA03618HLA00071HLA01759HLA05460HLA05706HLA06338HLA07669HLA07609HLA00072HLA01043HLA01511HLA02607HLA02669HLA03523HLA03565HLA03919HLA04061HLA04645HLA04762HLA04793HLA05915HLA05943HLA06190HLA08261HLA08262HLA08263HLA08264HLA08482HLA08615HLA09783HLA00073HLA02177HLA02180HLA02255HLA02828HLA03230HLA03583HLA03811HLA03876HLA03888HLA03891HLA04144HLA04586HLA05351HLA05315HLA05339HLA05448HLA05657HLA05941HLA05944HLA06021HLA06784HLA07583HLA07584HLA08120HLA08265HLA08613HLA09524HLA09525HLA00074HLA00075HLA04741HLA00076HLA00077HLA00078HLA00079HLA01805HLA00080HLA00081HLA00082HLA00083HLA00084HLA01044HLA01120HLA01272HLA01347HLA01351HLA01525HLA01796HLA01876HLA01894HLA01958HLA01966HLA02076HLA02156HLA02159HLA02367HLA02471HLA02521HLA02543HLA02581HLA02616HLA02640HLA02731HLA02939HLA03297HLA03329HLA03689HLA03793HLA03825HLA04143HLA04523HLA04726HLA04751HLA04785HLA05144HLA05312HLA05316HLA05341HLA05407HLA05642HLA05649HLA05702HLA05708HLA05709HLA05911HLA05929HLA06012HLA06018HLA06022HLA06191HLA06205HLA06209HLA06279HLA06283HLA06348HLA06542HLA06554HLA06808HLA07289HLA07393HLA07408HLA07670HLA07746HLA08023HLA08028HLA08256HLA08411HLA08598HLA08607HLA08900HLA08933HLA08946HLA08947HLA09474HLA09479HLA09490HLA09492HLA09499HLA09510HLA09526HLA09568HLA09784HLA09807HLA00085HLA01406HLA03528HLA05634HLA08026HLA00086HLA05528HLA01703HLA01887HLA03923HLA04140HLA05451HLA05902HLA05977HLA06795HLA07422HLA07570HLA08249HLA08255HLA00087HLA00088HLA01512HLA01558HLA01650HLA01696HLA01716HLA01795HLA01852HLA02083HLA02084HLA02256HLA02544HLA02733HLA03025HLA03467HLA03560HLA03916HLA04560HLA04584HLA05428HLA05438HLA05683HLA05903HLA05905HLA06151HLA06553HLA06783HLA06829HLA07392HLA07569HLA07666HLA07667HLA08027HLA08030HLA08031HLA08087HLA08092HLA08110HLA08245HLA08250HLA08253HLA08254HLA08600HLA08792HLA08810HLA08925HLA09113HLA09128HLA09162HLA09410HLA09520HLA09824HLA00089HLA01963HLA04809HLA05681HLA06743HLA08029HLA08269HLA00090HLA01943HLA02199HLA03142HLA04643HLA08037HLA08039HLA08268HLA08622HLA08623HLA09527HLA09547HLA00091HLA00092HLA05744HLA00094HLA00095HLA01112HLA01224HLA01411HLA01445HLA03102HLA01584HLA02102HLA02116HLA02127HLA02439HLA02510HLA02646HLA02760HLA02794HLA02980HLA02997HLA03097HLA03308HLA03502HLA03549HLA03564HLA03871HLA04138HLA04146HLA04522HLA04637HLA04651HLA04690HLA04850HLA04812HLA05251HLA05252HLA05331HLA05340HLA05452HLA05541HLA05551HLA05667HLA05652HLA06193HLA06194HLA06195HLA06201HLA06206HLA06543HLA06742HLA06749HLA06833HLA07395HLA07396HLA07397HLA07559HLA07586HLA07587HLA07751HLA07794HLA08036HLA08038HLA08267HLA08624HLA08775HLA08778HLA08789HLA08949HLA09160HLA09409HLA09465HLA09528HLA09529HLA09647HLA09705HLA00097HLA02945HLA04466HLA04467HLA04548HLA04740HLA05091HLA05100HLA06028HLA07421HLA07568HLA07811HLA08033HLA08251HLA08252HLA08939HLA09411HLA00098HLA00099HLA00100HLA01199HLA01546HLA01603HLA00066HLA01651HLA01970HLA02040HLA02085HLA02355HLA02651HLA02737HLA02898HLA02900HLA02934HLA03016HLA03116HLA03141HLA03292HLA03417HLA03570HLA03769HLA03920HLA03925HLA04418HLA04725HLA04746HLA04786HLA05241HLA05250HLA05302HLA05325HLA05345HLA05346HLA05447HLA05459HLA05522HLA05655HLA05666HLA05671HLA05682HLA05794HLA05799HLA05936HLA06122HLA06188HLA06337HLA06782HLA06794HLA06819HLA06837HLA07100HLA07338HLA07344HLA07390HLA07413HLA07522HLA07554HLA07775HLA08032HLA08034HLA08079HLA08093HLA08479HLA08608HLA08609HLA08610HLA08929HLA09156HLA09161HLA09447HLA09776HLA09777HLA09778HLA00101HLA02879HLA03046HLA04486HLA04813HLA05457HLA05946HLA05979HLA06335HLA06539HLA06757HLA07428HLA07805HLA08455HLA08938HLA00102HLA00103HLA01045HLA01207HLA01228HLA01463HLA01886HLA02138HLA02258HLA02413HLA02615HLA02649HLA02710HLA02798HLA03236HLA03495HLA03571HLA03783HLA03875HLA04642HLA04749HLA05121HLA05347HLA05349HLA05430HLA05632HLA05639HLA05641HLA05839HLA06007HLA06334HLA06371HLA08788HLA06378HLA06552HLA06789HLA07185HLA07603HLA07604HLA07606HLA07819HLA08035HLA08040HLA08047HLA08048HLA08284HLA08453HLA08454HLA08457HLA08458HLA08485HLA08491HLA08566HLA08570HLA08643HLA08969HLA08906HLA08970HLA09544HLA00104HLA03885HLA03926HLA05444HLA05660HLA06199HLA08480HLA00106HLA01758HLA03594HLA04141HLA04723HLA05242HLA06198HLA06204HLA07284HLA07523HLA08599HLA08787HLA08793HLA09322HLA09779HLA00107HLA00971HLA01318HLA01704HLA02250HLA02739HLA02807HLA02918HLA02959HLA02981HLA03221HLA03246HLA03286HLA03291HLA03349HLA08569HLA03388HLA03472HLA03498HLA03500HLA03566HLA03817HLA03915HLA03921HLA04057HLA04118HLA04549HLA05101HLA05367HLA05445HLA07565HLA05633HLA05656HLA05930HLA05965HLA06011HLA06055HLA06153HLA06181HLA06189HLA06330HLA06372HLA06738HLA06761HLA06817HLA06901HLA06904HLA07041HLA07043HLA07293HLA07296HLA07391HLA07524HLA07564HLA07566HLA07567HLA07795HLA08042HLA08049HLA08410HLA08611HLA08612HLA08971HLA09083HLA09089HLA09412HLA09521HLA09522HLA09775HLA00108HLA03011HLA00109HLA05942HLA07580HLA01248HLA01320HLA01675HLA01904HLA02363HLA02502HLA05637HLA08617HLA09336HLA00110HLA01290HLA01497HLA01631HLA04652HLA00111HLA00112HLA00113HLA00114HLA01375HLA02344HLA02472HLA03151HLA03416HLA03592HLA03775HLA04136HLA04531HLA04810HLA05143HLA05317HLA06066HLA08116HLA08483HLA08616HLA00115HLA05918HLA00116HLA01726HLA02327HLA02542HLA02889HLA02983HLA05443HLA05463HLA06192HLA07550HLA07582HLA07585HLA07671HLA07673HLA08046HLA08620HLA08945HLA09413HLA09712HLA00117HLA02508HLA02911HLA03152HLA04545HLA04547HLA07572HLA00118HLA00119HLA05557HLA00120HLA00121HLA00122HLA00123HLA00124HLA03519HLA00125HLA00972HLA09333HLA09659HLA09789HLA00973HLA01046HLA01047HLA08621HLA01048HLA01106HLA01119HLA01170HLA01291HLA01303HLA01464HLA01590HLA05984HLA01595HLA01652HLA01707HLA01822HLA01918HLA01944HLA09786HLA02103HLA02361HLA02364HLA02441HLA02470HLA02531HLA02595HLA02624HLA02701HLA02780HLA02859HLA02940HLA02982HLA03050HLA03171HLA03340HLA03533HLA03561HLA03581HLA03714HLA03816HLA04774HLA05123HLA05303HLA05328HLA05342HLA05350HLA05431HLA05437HLA05442HLA05446HLA05622HLA05645HLA05650HLA05690HLA05692HLA05700HLA05710HLA05869HLA05938HLA05961HLA05986HLA06013HLA06129HLA06200HLA06340HLA06343HLA06349HLA09787HLA06537HLA06540HLA06541HLA06748HLA06739HLA06796HLA06806HLA06836HLA07290HLA07350HLA07571HLA07581HLA07773HLA08043HLA08044HLA08045HLA08051HLA08057HLA08282HLA08619HLA08803HLA08940HLA08948HLA09108HLA00126HLA09785HLA00127HLA00128HLA05527HLA00129HLA01115HLA01254HLA01422HLA01519HLA01544HLA01653HLA01819HLA02254HLA02379HLA03499HLA03771HLA05967HLA08280HLA08456HLA00130HLA08791HLA04682HLA09134HLA00132HLA00133HLA00134HLA01763HLA02949HLA02990HLA03089HLA03720HLA03772HLA03900HLA03938HLA04042HLA04058HLA04113HLA04191HLA04198HLA04238HLA04246HLA04571HLA05253HLA06678HLA06679HLA06702HLA06703HLA06871HLA06922HLA06924HLA06981HLA07207HLA07467HLA07661HLA07722HLA08136HLA08379HLA08385HLA08685HLA08686HLA09006HLA09724HLA00135HLA00136HLA00137HLA02317HLA02329HLA04781HLA05390HLA05716HLA00138HLA00139HLA00140HLA00141HLA00142HLA04861HLA04924HLA04925HLA04929HLA04931HLA04933HLA04935HLA04964HLA04966HLA04981HLA00143HLA04993HLA05000HLA04884HLA04886HLA05094HLA05095HLA05106HLA05531HLA06041HLA06061HLA00144HLA06131HLA06187HLA06224HLA06225HLA06285HLA06317HLA06318HLA06319HLA06586HLA06658HLA00145HLA06659HLA06677HLA06690HLA06691HLA06905HLA06923HLA06970HLA06980HLA07035HLA07039HLA01049HLA07205HLA07206HLA07208HLA07305HLA07354HLA07465HLA07466HLA07468HLA07469HLA07659HLA01050HLA07660HLA07662HLA07721HLA07723HLA07724HLA08050HLA08052HLA08134HLA08135HLA08137HLA01051HLA08138HLA08293HLA08305HLA08380HLA08381HLA08382HLA08383HLA08384HLA08386HLA08443HLA01110HLA08470HLA08520HLA08521HLA08522HLA08523HLA08567HLA08684HLA08934HLA09005HLA09007HLA09008HLA09009HLA09116HLA09172HLA09318HLA09338HLA09430HLA09443HLA09444HLA09445HLA01116HLA03088HLA01176HLA09446HLA09487HLA09491HLA09493HLA09588HLA09589HLA09590HLA09591HLA09592HLA01184HLA01253HLA01257HLA03260HLA01286HLA01293HLA01358HLA01362HLA01435HLA01516HLA01548HLA01577HLA01618HLA01725HLA01742HLA09701HLA01750HLA01783HLA01808HLA01881HLA01883HLA02089HLA02129HLA02164HLA02175HLA02247HLA02350HLA02393HLA02446HLA02463HLA02514HLA02519HLA02560HLA02713HLA02796HLA02805HLA02844HLA02873HLA02910HLA07464HLA02968HLA02978HLA02991HLA03137HLA03166HLA03179HLA03237HLA03264HLA03294HLA03342HLA03413HLA03514HLA05222HLA06826HLA03605HLA03610HLA03611HLA03622HLA03658HLA03660HLA03679HLA03692HLA03761HLA03933HLA03934HLA03936HLA03937HLA03940HLA03942HLA04067HLA04074HLA04079HLA04092HLA04097HLA04099HLA04109HLA03981HLA04172HLA04193HLA04219HLA04233HLA04241HLA05512HLA04243HLA04248HLA04250HLA00146HLA02219HLA02400HLA02853HLA03134HLA03449HLA03939HLA04210HLA04221HLA04504HLA05127HLA05362HLA05482HLA06132HLA06215HLA06917HLA07637HLA08341HLA08665HLA08776HLA09558HLA00147HLA00148HLA00149HLA00150HLA00974HLA00975HLA00976HLA01082HLA08510HLA08581HLA08666HLA08668HLA08669HLA08784HLA09112HLA09429HLA09450HLA09512HLA01193HLA09557HLA09874HLA01230HLA03935HLA04186HLA01352HLA01418HLA01535HLA01641HLA01654HLA01701HLA01717HLA01752HLA01772HLA01917HLA02132HLA02142HLA02252HLA02308HLA02406HLA02490HLA02496HLA02591HLA02762HLA02771HLA02849HLA03091HLA03164HLA03265HLA03450HLA03481HLA03663HLA03648HLA03902HLA03941HLA04081HLA04188HLA04230HLA04234HLA04240HLA04438HLA04442HLA04499HLA04507HLA04515HLA04516HLA08667HLA04520HLA04708HLA04720HLA08338HLA04722HLA04753HLA04788HLA08983HLA04816HLA04860HLA05290HLA05506HLA05510HLA05720HLA05861HLA06258HLA06259HLA06260HLA06664HLA06682HLA06918HLA06928HLA06943HLA06956HLA06984HLA06996HLA07191HLA07386HLA07418HLA07442HLA07443HLA07444HLA07445HLA07446HLA07635HLA07636HLA07638HLA08041HLA07911HLA07912HLA07913HLA08097HLA08141HLA08339HLA08340HLA08343HLA08508HLA08509HLA00152HLA03770HLA04580HLA05254HLA05255HLA06374HLA00153HLA02174HLA02295HLA02809HLA03599HLA04083HLA04849HLA05256HLA05413HLA06235HLA06699HLA06957HLA07917HLA08346HLA08347HLA00154HLA00155HLA01276HLA01309HLA01476HLA01486HLA01591HLA01632HLA01840HLA08902HLA01858HLA02360HLA02389HLA02516HLA02619HLA02872HLA02929HLA02930HLA03138HLA03315HLA03591HLA03479HLA03834HLA03944HLA04107HLA03982HLA04195HLA04207HLA04436HLA04414HLA04502HLA04554HLA04567HLA04650HLA04787HLA05118HLA05134HLA05809HLA06024HLA06056HLA06149HLA06236HLA06263HLA06264HLA06933HLA06958HLA06975HLA07033HLA07094HLA07105HLA07693HLA07694HLA07892HLA07915HLA07916HLA08058HLA08345HLA08573HLA08574HLA08671HLA08790HLA09155HLA09431HLA09442HLA09456HLA09501HLA09645HLA00157HLA05490HLA09174HLA00158HLA02150HLA04101HLA04496HLA04415HLA05878HLA08311HLA09004HLA09341HLA00159HLA00160HLA00161HLA00977HLA01052HLA02166HLA03283HLA03318HLA03639HLA03664HLA04027HLA04055HLA04066HLA04176HLA04192HLA04532HLA04565HLA05474HLA05928HLA05960HLA06324HLA06325HLA06357HLA06950HLA06990HLA07004HLA07190HLA07463HLA07658HLA07717HLA07725HLA08376HLA09585HLA09586HLA09587HLA09699HLA00162HLA00163HLA00164HLA00978HLA01373HLA03005HLA03184HLA03215HLA03964HLA04071HLA04112HLA04216HLA04454HLA04463HLA04464HLA04553HLA05257HLA05405HLA05718HLA05819HLA06133HLA06154HLA06888HLA06966HLA07457HLA07458HLA07525HLA07709HLA08071HLA08369HLA08678HLA09175HLA09575HLA00165HLA04201HLA04471HLA04473HLA05501HLA07924HLA00166HLA03954HLA03958HLA08907HLA00167HLA00168HLA04569HLA00169HLA00170HLA05261HLA00171HLA00172HLA02140HLA02184HLA02236HLA02244HLA02330HLA02332HLA02368HLA02376HLA02387HLA00173HLA04448HLA02421HLA02454HLA02465HLA02483HLA02492HLA02515HLA02545HLA02618HLA02639HLA02642HLA00174HLA01201HLA02673HLA04157HLA05262HLA00175HLA02665HLA02674HLA02759HLA02772HLA02773HLA02781HLA02792HLA02823HLA02875HLA02882HLA02974HLA02976HLA03019HLA03047HLA03080HLA03087HLA03092HLA03093HLA03094HLA00176HLA06965HLA00177HLA03202HLA03217HLA03244HLA03267HLA03269HLA03281HLA03287HLA03319HLA03334HLA03348HLA00178HLA03441HLA03470HLA03603HLA03606HLA03614HLA03615HLA03620HLA03646HLA03693HLA03708HLA03711HLA03804HLA03951HLA03947HLA03949HLA04052HLA04078HLA04084HLA03985HLA03990HLA00179HLA06327HLA06992HLA04028HLA04169HLA04171HLA04187HLA04213HLA04218HLA04232HLA04242HLA04158HLA04159HLA00180HLA01439HLA02141HLA04165HLA04457HLA04458HLA04508HLA04533HLA04413HLA04635HLA04684HLA04727HLA04742HLA00181HLA04093HLA04023HLA04500HLA08372HLA00182HLA04770HLA04792HLA05135HLA05258HLA05259HLA05260HLA05263HLA05264HLA05265HLA05266HLA00183HLA05369HLA05380HLA05381HLA05471HLA05479HLA05489HLA05500HLA05509HLA05516HLA05810HLA00184HLA05953HLA05957HLA06030HLA06031HLA06032HLA06033HLA06184HLA06222HLA06248HLA06267HLA06273HLA06282HLA06366HLA06652HLA06654HLA06680HLA06885HLA06893HLA06903HLA06921HLA00186HLA06930HLA06947HLA06948HLA06988HLA06997HLA07093HLA07179HLA07385HLA07412HLA07453HLA07649HLA07650HLA07653HLA07712HLA07713HLA07918HLA07928HLA07933HLA08068HLA08069HLA00187HLA09307HLA08070HLA08072HLA08074HLA08075HLA08144HLA08321HLA08368HLA08405HLA08409HLA08417HLA00188HLA03906HLA05857HLA08514HLA08515HLA08578HLA08595HLA08783HLA08926HLA09000HLA09074HLA08996HLA09120HLA00189HLA09159HLA09329HLA09437HLA09438HLA09440HLA09454HLA09517HLA09573HLA09574HLA09576HLA00190HLA03103HLA03302HLA00191HLA09578HLA09695HLA09708HLA00192HLA00193HLA00194HLA00195HLA00196HLA00197HLA00198HLA00199HLA00200HLA00201HLA04190HLA00202HLA05472HLA00203HLA00205HLA00206HLA00207HLA00208HLA00209HLA00210HLA07652HLA00211HLA00212HLA00979HLA00980HLA01053HLA01054HLA01103HLA01113HLA01114HLA01117HLA01118HLA01200HLA01250HLA01271HLA01284HLA01285HLA08373HLA01426HLA01440HLA01448HLA01479HLA01494HLA01536HLA01561HLA01567HLA01611HLA01679HLA01690HLA01698HLA01743HLA01751HLA03961HLA06919HLA01767HLA01768HLA01792HLA01801HLA01845HLA01900HLA01911HLA01912HLA01913HLA01915HLA01916HLA01950HLA01951HLA01975HLA01989HLA01999HLA02032HLA02035HLA02099HLA02113HLA02119HLA00213HLA07768HLA01565HLA02650HLA04189HLA04249HLA04432HLA04453HLA04566HLA05483HLA06233HLA06234HLA06354HLA06358HLA06380HLA07633HLA07691HLA07909HLA08664HLA00214HLA00215HLA00216HLA00217HLA00218HLA00219HLA04075HLA01055HLA01131HLA01177HLA01270HLA01281HLA01353HLA01506HLA01508HLA01532HLA01613HLA01782HLA01914HLA02315HLA02388HLA02698HLA02699HLA02783HLA02851HLA02995HLA03180HLA03263HLA03462HLA03463HLA03510HLA03612HLA03717HLA03946HLA03956HLA03957HLA04088HLA04091HLA04106HLA04202HLA04205HLA04212HLA04222HLA07910HLA04223HLA04445HLA04510HLA04752HLA04805HLA05125HLA05485HLA05508HLA06063HLA06135HLA06185HLA06213HLA06214HLA06232HLA06243HLA06322HLA06575HLA06581HLA06660HLA06825HLA06927HLA06995HLA07189HLA07303HLA07632HLA07679HLA07809HLA07904HLA07905HLA07906HLA07907HLA07908HLA08335HLA08336HLA08392HLA08403HLA08438HLA08506HLA08663HLA08936HLA08982HLA09077HLA09345HLA09427HLA09428HLA09513HLA09556HLA00220HLA00221HLA06955HLA00222HLA00223HLA02246HLA03987HLA00225HLA00226HLA01179HLA01642HLA01635HLA01985HLA02100HLA02218HLA02826HLA04054HLA04197HLA04509HLA05400HLA05477HLA05925HLA06926HLA07634HLA07901HLA08661HLA08979HLA08980HLA00227HLA00228HLA07340HLA08329HLA00229HLA00230HLA00231HLA08911HLA09308HLA09309HLA09326HLA09426HLA09452HLA09703HLA00232HLA00233HLA00234HLA00235HLA00236HLA01056HLA01130HLA01143HLA01147HLA01173HLA01277HLA01348HLA01504HLA01529HLA01952HLA02023HLA02118HLA02171HLA02238HLA02301HLA02370HLA02437HLA02473HLA02499HLA02513HLA02784HLA02931HLA03176HLA03200HLA03276HLA03278HLA03323HLA03551HLA03554HLA03616HLA03659HLA03661HLA03677HLA03712HLA03810HLA03824HLA03952HLA03955HLA04048HLA04053HLA04089HLA04175HLA04164HLA04443HLA04449HLA04564HLA04715HLA04769HLA04771HLA05267HLA05404HLA05268HLA05269HLA05473HLA05492HLA05504HLA05517HLA06183HLA06212HLA06230HLA06255HLA06256HLA06292HLA06353HLA06940HLA06993HLA07187HLA07188HLA07177HLA07339HLA07441HLA07631HLA07689HLA07902HLA08505HLA07903HLA07932HLA08327HLA08330HLA08331HLA08332HLA08472HLA08504HLA08662HLA00237HLA05354HLA01264HLA02121HLA02176HLA02313HLA02566HLA03288HLA03796HLA03963HLA04114HLA04179HLA04181HLA04237HLA04434HLA04446HLA04468HLA04474HLA04521HLA04544HLA05270HLA05271HLA05817HLA06139HLA06580HLA06583HLA06651HLA06689HLA06906HLA07003HLA07644HLA07704HLA08358HLA08435HLA08357HLA08513HLA08676HLA08992HLA09571HLA00238HLA02143HLA03476HLA04582HLA08564HLA00239HLA03607HLA04437HLA04789HLA05491HLA05535HLA05841HLA06148HLA06220HLA06961HLA07705HLA08677HLA00240HLA02260HLA03337HLA00241HLA04820HLA07792HLA00242HLA00243HLA00244HLA02506HLA03104HLA04178HLA07335HLA08512HLA00245HLA00246HLA07178HLA00247HLA04900HLA04904HLA04959HLA04864HLA04907HLA04910HLA04911HLA04913HLA04914HLA04916HLA04921HLA04919HLA05063HLA04922HLA04923HLA04882HLA04932HLA04936HLA04938HLA04941HLA04866HLA04946HLA00248HLA05273HLA08393HLA04960HLA04961HLA04962HLA04963HLA04965HLA04967HLA04978HLA04980HLA04992HLA04998HLA00249HLA04183HLA06647HLA00250HLA04999HLA05009HLA04867HLA04872HLA04874HLA04879HLA04888HLA04892HLA05047HLA05051HLA05056HLA05058HLA05059HLA05060HLA05061HLA05272HLA05713HLA05814HLA05826HLA05828HLA00251HLA01741HLA00252HLA05830HLA05835HLA05955HLA05983HLA05997HLA06057HLA06134HLA06239HLA06261HLA06266HLA00253HLA06278HLA06376HLA06574HLA06648HLA06684HLA06685HLA06686HLA06815HLA06884HLA06929HLA00254HLA06935HLA06945HLA06946HLA06960HLA06962HLA06964HLA06977HLA06987HLA06999HLA07196HLA00255HLA07197HLA07198HLA07202HLA07212HLA07302HLA05274HLA07325HLA07452HLA07549HLA07560HLA00256HLA07645HLA07646HLA07651HLA07692HLA07701HLA07703HLA07706HLA07719HLA07769HLA07780HLA07796HLA07914HLA07927HLA07939HLA08062HLA08063HLA08108HLA08316HLA08319HLA08344HLA00257HLA03014HLA00258HLA08354HLA08356HLA08397HLA08359HLA08360HLA08361HLA08362HLA08499HLA08507HLA08785HLA00259HLA08804HLA08990HLA08991HLA08993HLA08994HLA09003HLA09098HLA09139HLA09435HLA09436HLA00260HLA09504HLA09709HLA09697HLA00261HLA04497HLA00262HLA00263HLA00264HLA00981HLA00982HLA07454HLA01057HLA01058HLA01059HLA07195HLA01060HLA01194HLA01202HLA01296HLA01314HLA01503HLA01509HLA01550HLA01563HLA01578HLA04675HLA00185HLA01182HLA01668HLA01727HLA01846HLA01850HLA01888HLA01896HLA01897HLA01984HLA01990HLA02016HLA02031HLA02038HLA02091HLA02128HLA02134HLA02228HLA02251HLA08782HLA02385HLA02399HLA02402HLA08317HLA02411HLA02480HLA02489HLA02645HLA03262HLA02694HLA02734HLA02756HLA02763HLA02810HLA02847HLA02909HLA02977HLA03003HLA03008HLA03078HLA03084HLA03125HLA03126HLA03149HLA03169HLA03197HLA03198HLA03210HLA03300HLA03321HLA03324HLA03335HLA03336HLA03343HLA03625HLA03662HLA03644HLA03722HLA03715HLA00265HLA02418HLA02505HLA02687HLA03651HLA03908HLA04184HLA06994HLA08333HLA00266HLA01267HLA01346HLA04738HLA01359HLA01949HLA02007HLA02015HLA02149HLA02231HLA02479HLA02532HLA02874HLA03350HLA03959HLA04073HLA04208HLA04229HLA04160HLA04511HLA04539HLA04692HLA05421HLA05487HLA05719HLA06182HLA06231HLA06257HLA06321HLA06916HLA06941HLA07552HLA07690HLA07931HLA08334HLA08337HLA08779HLA00267HLA02477HLA04090HLA04217HLA05962HLA07471HLA07727HLA00268HLA00269HLA05525HLA08572HLA09455HLA00270HLA01137HLA01219HLA01265HLA01294HLA01515HLA01655HLA01923HLA02161HLA02394HLA02504HLA02584HLA02714HLA02806HLA03051HLA03590HLA03694HLA04076HLA04439HLA04475HLA05301HLA05519HLA05712HLA05843HLA06242HLA06316HLA06326HLA06585HLA06692HLA06830HLA06834HLA06971HLA06991HLA07211HLA07310HLA07470HLA07718HLA07720HLA08389HLA08390HLA09131HLA00271HLA02220HLA08053HLA00273HLA01123HLA03314HLA03473HLA04041HLA04043HLA04050HLA04177HLA04730HLA05514HLA08139HLA08283HLA08597HLA09085HLA00274HLA00275HLA00276HLA00277HLA00278HLA04440HLA00279HLA00280HLA09593HLA00281HLA00282HLA00283HLA00284HLA06931HLA00285HLA00286HLA00287HLA02165HLA00288HLA00289HLA00290HLA01061HLA01128HLA01133HLA03275HLA01183HLA01196HLA01203HLA01221HLA06320HLA01493HLA01528HLA01656HLA01789HLA01920HLA01924HLA01926HLA01927HLA02097HLA02163HLA02331HLA02378HLA02384HLA02412HLA02426HLA07781HLA02436HLA08388HLA02457HLA02926HLA03006HLA03338HLA03341HLA03542HLA03621HLA03647HLA03747HLA03756HLA04072HLA04105HLA04200HLA04161HLA04451HLA04472HLA04796HLA05275HLA05276HLA05292HLA05511HLA05714HLA06271HLA06938HLA06951HLA06952HLA06953HLA07307HLA07472HLA07663HLA07664HLA07665HLA07726HLA08140HLA08142HLA08322HLA08412HLA08469HLA08524HLA09010HLA09011HLA09173HLA09570HLA00291HLA00292HLA01450HLA01800HLA01921HLA03153HLA04070HLA04170HLA04728HLA04846HLA05278HLA05280HLA05467HLA05493HLA05520HLA05804HLA05815HLA05924HLA06210HLA06253HLA06695HLA06696HLA06973HLA07439HLA07925HLA08301HLA08439HLA08500HLA08501HLA00293HLA01996HLA02262HLA03633HLA03757HLA04174HLA04220HLA04543HLA04648HLA04818HLA05283HLA06155HLA07628HLA07687HLA07688HLA08328HLA08503HLA00294HLA00295HLA00296HLA00297HLA01430HLA02077HLA05355HLA06882HLA07630HLA08594HLA09153HLA00298HLA00299HLA00300HLA04901HLA04902HLA04903HLA04912HLA04915HLA04917HLA04918HLA04920HLA05153HLA04930HLA00301HLA05393HLA04880HLA04934HLA04937HLA04939HLA04940HLA04947HLA04977HLA04979HLA04997HLA05010HLA00302HLA05126HLA00303HLA05011HLA05018HLA05021HLA04868HLA05151HLA05391HLA05152HLA04873HLA04875HLA04877HLA04878HLA00304HLA04881HLA05050HLA05053HLA05054HLA05093HLA05096HLA05097HLA05154HLA05277HLA05279HLA05281HLA05282HLA05284HLA05285HLA05286HLA05305HLA05363HLA05410HLA05537HLA05695HLA00305HLA01667HLA01816HLA00306HLA05803HLA05805HLA05811HLA05816HLA05824HLA05842HLA05856HLA05859HLA05866HLA06025HLA00307HLA06228HLA08325HLA06281HLA06302HLA06314HLA06653HLA06681HLA06693HLA06887HLA06914HLA06915HLA06939HLA06972HLA06982HLA06983HLA07095HLA07285HLA07286HLA07304HLA07332HLA07378HLA00309HLA07384HLA07440HLA07625HLA07626HLA07629HLA07680HLA07681HLA07682HLA07684HLA07685HLA00310HLA07686HLA07728HLA07754HLA07762HLA07890HLA07891HLA07893HLA07894HLA07895HLA07896HLA00311HLA07897HLA07898HLA07899HLA07900HLA07919HLA07920HLA07921HLA07962HLA08101HLA08102HLA00983HLA08105HLA08106HLA08112HLA08315HLA08287HLA08296HLA08302HLA08323HLA08326HLA08353HLA08396HLA08407HLA08577HLA08579HLA08658HLA08659HLA08660HLA08879HLA08884HLA08928HLA00984HLA01062HLA08931HLA08976HLA08978HLA09101HLA09423HLA09425HLA09457HLA09461HLA09475HLA09483HLA01063HLA09555HLA09700HLA09702HLA09704HLA01064HLA01122HLA01129HLA05954HLA01140HLA01223HLA01232HLA01246HLA01269HLA01287HLA01299HLA01329HLA01482HLA01488HLA01490HLA01495HLA01510HLA01527HLA01600HLA01604HLA01702HLA01740HLA01748HLA01765HLA01898HLA01899HLA01919HLA01976HLA01979HLA01992HLA01993HLA01994HLA01995HLA02217HLA02227HLA02229HLA02249HLA02383HLA02458HLA02482HLA02498HLA02536HLA02588HLA02597HLA02678HLA02693HLA02799HLA02850HLA03344HLA02864HLA02866HLA02884HLA02906HLA02913HLA02989HLA03160HLA03173HLA03205HLA03220HLA03222HLA03231HLA03243HLA03245HLA03256HLA06280HLA03270HLA03311HLA03312HLA03339HLA03392HLA03403HLA03584HLA03628HLA03602HLA03746HLA03780HLA04387HLA00312HLA00313HLA03965HLA05515HLA06697HLA09424HLA00314HLA02922HLA01256HLA01288HLA01452HLA02144HLA02300HLA03905HLA04094HLA04236HLA04247HLA05505HLA05538HLA05533HLA05833HLA06059HLA06252HLA06694HLA07624HLA08290HLA08502HLA08654HLA08655HLA08657HLA08975HLA09310HLA09554HLA00315HLA04227HLA08394HLA00316HLA01524HLA01712HLA01939HLA01941HLA02311HLA02390HLA02643HLA03645HLA03823HLA03945HLA04168HLA05308HLA06223HLA06286HLA07959HLA08981HLA09314HLA09313HLA00318HLA01606HLA08401HLA01247HLA01487HLA02684HLA03412HLA03953HLA03960HLA03948HLA04116HLA04196HLA04534HLA04568HLA04714HLA05721HLA06000HLA06217HLA06304HLA06646HLA06985HLA06998HLA07032HLA07450HLA07639HLA07641HLA08123HLA08519HLA08601HLA09433HLA09434HLA00319HLA00320HLA02825HLA03840HLA03907HLA04103HLA04013HLA04252HLA04754HLA04815HLA04847HLA05481HLA06262HLA06645HLA07695HLA08089HLA08350HLA08352HLA08471HLA00321HLA00322HLA04563HLA06944HLA08132HLA00323HLA00324HLA00325HLA00326HLA00327HLA04994HLA04889HLA05048HLA05049HLA05052HLA05055HLA05057HLA05062HLA05092HLA05099HLA00328HLA05406HLA05534HLA05717HLA05829HLA05858HLA05877HLA05926HLA06045HLA06156HLA06216HLA01065HLA06218HLA06237HLA06244HLA06245HLA06246HLA06247HLA06265HLA08125HLA06301HLA06323HLA06578HLA01066HLA06642HLA06954HLA06976HLA07087HLA06986HLA07090HLA07193HLA07194HLA07343HLA07388HLA01067HLA07447HLA07448HLA07449HLA07451HLA07640HLA07642HLA07696HLA07697HLA07698HLA07700HLA01068HLA07767HLA07808HLA07812HLA08060HLA08061HLA08131HLA08342HLA08348HLA08349HLA08351HLA01146HLA08432HLA08511HLA08672HLA08674HLA08683HLA08687HLA08809HLA08937HLA08984HLA08985HLA01148HLA08986HLA08987HLA08988HLA09169HLA09305HLA09432HLA09559HLA09594HLA09595HLA09696HLA01144HLA09706HLA09711HLA01187HLA01195HLA01197HLA01313HLA01341HLA01354HLA01427HLA01449HLA01489HLA06289HLA01521HLA03203HLA01526HLA01530HLA01569HLA01617HLA01691HLA01700HLA08517HLA01713HLA01784HLA01790HLA07699HLA01797HLA01804HLA01986HLA02098HLA06152HLA02206HLA02234HLA05860HLA02309HLA02316HLA02343HLA02464HLA02644HLA02675HLA02695HLA02700HLA02770HLA02883HLA02941HLA03001HLA03130HLA03133HLA03161HLA03190HLA08673HLA03259HLA03345HLA03358HLA03359HLA03360HLA03393HLA03536HLA03601HLA03627HLA03718HLA03695HLA03903HLA03950HLA03962HLA03973HLA03974HLA04044HLA04056HLA04082HLA04085HLA04086HLA04096HLA04014HLA04022HLA04111HLA04173HLA04194HLA04215HLA04224HLA04228HLA04455HLA04460HLA04501HLA04514HLA04519HLA04526HLA04536HLA04540HLA04541HLA04542HLA04556HLA00329HLA00330HLA01229HLA01343HLA01419HLA01607HLA01940HLA03258HLA03299HLA04051HLA04481HLA05304HLA05825HLA07683HLA00331HLA02685HLA04503HLA04734HLA05818HLA05956HLA06360HLA09157HLA09340HLA01139HLA01977HLA01980HLA02211HLA02296HLA02298HLA02336HLA02736HLA02808HLA02905HLA03086HLA03249HLA03613HLA04743HLA03271HLA03357HLA03361HLA03442HLA03512HLA03778HLA03909HLA03966HLA05480HLA04163HLA05287HLA05412HLA05812HLA05813HLA06313HLA06889HLA07280HLA07306HLA07961HLA08314HLA08247HLA08285HLA08398HLA08587HLA08563HLA08805HLA09488HLA09583HLA09821HLA00332HLA01437HLA06062HLA00333HLA00334HLA01481HLA01953HLA04709HLA04790HLA06219HLA00335HLA02767HLA05376HLA08901HLA00336HLA04461HLA08378HLA00337HLA02727HLA00338HLA00339HLA00986HLA01069HLA01777HLA01981HLA01982HLA02104HLA02112HLA02200HLA02377HLA02503HLA02517HLA02952HLA02965HLA03020HLA04245HLA04433HLA04750HLA05288HLA05475HLA06130HLA07209HLA07210HLA08143HLA08903HLA09087HLA09505HLA00340HLA03464HLA06211HLA08584HLA01252HLA01266HLA02209HLA02342HLA04098HLA04128HLA04535HLA04538HLA04706HLA05484HLA05496HLA05498HLA05722HLA05834HLA06227HLA06352HLA06891HLA06925HLA06932HLA07958HLA08122HLA08324HLA08606HLA08670HLA09167HLA00341HLA04100HLA06254HLA00342HLA01070HLA04049HLA04108HLA04180HLA04182HLA04239HLA05466HLA05470HLA05499HLA06238HLA06835HLA07186HLA07627HLA07968HLA08559HLA08656HLA08894HLA08977HLA09316HLA09818HLA00344HLA00345HLA01126HLA01149HLA01579HLA02117HLA02232HLA02924HLA03273HLA03797HLA04059HLA04206HLA04235HLA04505HLA04513HLA04551HLA04707HLA05469HLA05494HLA05715HLA05998HLA06023HLA06157HLA06251HLA06288HLA06364HLA06936HLA06979HLA07319HLA07203HLA07654HLA07655HLA07656HLA07716HLA08395HLA08525HLA08575HLA08680HLA08880HLA09002HLA09154HLA09584HLA00346HLA00347HLA02967HLA03505HLA06158HLA00348HLA00349HLA00350HLA00351HLA06268HLA00352HLA04729HLA00353HLA00354HLA03105HLA00355HLA05495HLA05536HLA05694HLA05840HLA05806HLA05836HLA05912HLA05959HLA06269HLA06270HLA06356HLA06365HLA06369HLA06579HLA06675HLA06676HLA06698HLA06701HLA06816HLA06959HLA00356HLA00357HLA06969HLA07001HLA07002HLA07180HLA07181HLA07204HLA07308HLA07461HLA07462HLA07623HLA07714HLA07715HLA07960HLA07964HLA08076HLA08077HLA08078HLA08130HLA08374HLA08375HLA00358HLA01127HLA00359HLA08377HLA08391HLA08414HLA08436HLA08568HLA08653HLA08681HLA08682HLA08780HLA08910HLA00360HLA09001HLA09317HLA09441HLA09489HLA09582HLA00361HLA01071HLA01072HLA01073HLA01132HLA01134HLA01243HLA01245HLA01262HLA03272HLA04518HLA05723HLA01417HLA01474HLA01537HLA01568HLA01621HLA01626HLA01657HLA01676HLA01678HLA01983HLA02003HLA02020HLA02167HLA02297HLA02419HLA02455HLA02558HLA02620HLA02667HLA02672HLA02754HLA02885HLA02933HLA03099HLA03123HLA03178HLA03277HLA03279HLA03282HLA03313HLA05999HLA03355HLA03456HLA03460HLA03465HLA03468HLA08107HLA03516HLA03509HLA03608HLA03617HLA03665HLA03674HLA03676HLA03716HLA03719HLA03901HLA03971HLA03972HLA04045HLA04080HLA04102HLA04104HLA04015HLA07553HLA04199HLA04204HLA04225HLA04231HLA04251HLA04166HLA04441HLA04444HLA04495HLA04537HLA04649HLA04704HLA04705HLA04711HLA04716HLA04718HLA04791HLA05289HLA05464HLA05468HLA05488HLA00362HLA05917HLA00363HLA01231HLA01677HLA04115HLA05486HLA05927HLA06159HLA06221HLA07103HLA07707HLA08065HLA08364HLA08366HLA08434HLA08675HLA08989HLA01141HLA01295HLA01580HLA01627HLA01964HLA03009HLA02196HLA02212HLA02452HLA02585HLA06978HLA02793HLA03293HLA03317HLA03354HLA03970HLA04162HLA04450HLA04459HLA04498HLA04733HLA05223HLA05497HLA06026HLA06355HLA06963HLA07000HLA07336HLA07823HLA07800HLA08064HLA08363HLA00364HLA01922HLA02114HLA02635HLA04244HLA07643HLA07702HLA09084HLA00365HLA00366HLA00987HLA01178HLA01261HLA01319HLA01484HLA04517HLA01522HLA02078HLA02352HLA02636HLA02942HLA03186HLA03209HLA03274HLA03595HLA06050HLA03609HLA04095HLA04462HLA04412HLA04713HLA04817HLA05862HLA06687HLA06934HLA07192HLA08066HLA08355HLA09439HLA09681HLA00367HLA06160HLA07966HLA09138HLA01204HLA02027HLA02095HLA02096HLA02079HLA02179HLA02398HLA02679HLA02716HLA02751HLA02752HLA02944HLA03356HLA03387HLA03480HLA03508HLA03748HLA03841HLA04719HLA04732HLA04735HLA05401HLA06284HLA07535HLA07758HLA07963HLA08576HLA09500HLA09879HLA00368HLA02137HLA02324HLA02335HLA04185HLA04214HLA06186HLA07201HLA07657HLA08679HLA09581HLA00369HLA02407HLA03513HLA04017HLA04167HLA05112HLA00370HLA00371HLA00372HLA00374HLA00375HLA01180HLA01205HLA01507HLA01553HLA01722HLA01732HLA01749HLA01788HLA02092HLA02093HLA02122HLA02320HLA02518HLA02539HLA02671HLA02677HLA02782HLA02845HLA02925HLA03098HLA03195HLA03228HLA03322HLA03366HLA03424HLA03503HLA03967HLA04047HLA03983HLA04211HLA04512HLA04821HLA05294HLA05295HLA05296HLA05478HLA05507HLA05756HLA05802HLA05807HLA06053HLA06519HLA06584HLA06920HLA06967HLA07314HLA07459HLA07710HLA08297HLA08962HLA09580HLA00376HLA04209HLA04552HLA04819HLA08998HLA09722HLA00377HLA00378HLA00379HLA00380HLA01719HLA00988HLA00989HLA01564HLA01625HLA01658HLA01688HLA01764HLA01892HLA02002HLA02043HLA02261HLA02565HLA02691HLA02757HLA02852HLA06968HLA03085HLA03266HLA03257HLA03511HLA04077HLA04024HLA04555HLA04768HLA04806HLA05502HLA06060HLA06650HLA07460HLA07711HLA07764HLA08059HLA08516HLA08518HLA08999HLA09579HLA09710HLA00381HLA01520HLA02259HLA03969HLA04060HLA04456HLA04755HLA05320HLA05465HLA05563HLA06363HLA07200HLA07801HLA08370HLA09723HLA00382HLA04435HLA00383HLA01289HLA00384HLA00385HLA01074HLA01192HLA01461HLA01485HLA02307HLA02676HLA02888HLA02966HLA03129HLA03147HLA03150HLA03320HLA03506HLA03507HLA03666HLA03675HLA03904HLA04046HLA03984HLA03986HLA04203HLA04452HLA04401HLA04576HLA04703HLA04848HLA05424HLA05476HLA05503HLA05513HLA05562HLA05876HLA05958HLA06229HLA06240HLA06241HLA06249HLA06250HLA06315HLA06683HLA06688HLA06700HLA06883HLA06942HLA06949HLA06974HLA06989HLA07455HLA07456HLA07545HLA07708HLA07748HLA08073HLA08294HLA08371HLA08927HLA08997HLA09303HLA09312HLA09577HLA00386HLA03248HLA04226HLA04388HLA05298HLA05370HLA05411HLA05518HLA06161HLA07647HLA07648HLA08406HLA00387HLA01142HLA01181HLA01312HLA01680HLA01723HLA06831HLA01728HLA02004HLA02201HLA02512HLA02596HLA02712HLA02880HLA03148HLA09572HLA03289HLA03316HLA03369HLA03471HLA03637HLA03968HLA04087HLA04025HLA04506HLA04397HLA04573HLA04641HLA05297HLA05742HLA06058HLA06226HLA06649HLA07199HLA07309HLA08067HLA08365HLA08367HLA08995HLA09302HLA09315HLA09328HLA09664HLA09684HLA09698HLA00389HLA06075HLA02589HLA03367HLA03537HLA03762HLA09482HLA00390HLA00391HLA09146HLA01374HLA05808HLA00392HLA05386HLA00393HLA06937HLA00394HLA00395HLA00396HLA00990HLA01403HLA03368HLA04712HLA00398HLA01809HLA03049HLA03261HLA05306HLA08387HLA00399HLA01188HLA04447HLA01135HLA00401HLA01798HLA02044HLA02670HLA02815HLA03445HLA03730HLA04275HLA04606HLA05209HLA05417HLA05781HLA05881HLA06162HLA07542HLA08145HLA08440HLA08885HLA09596HLA00402HLA01075HLA01434HLA01555HLA01644HLA01636HLA01659HLA01866HLA02123HLA02469HLA02478HLA02790HLA02811HLA02812HLA02813HLA02814HLA02947HLA03233HLA03303HLA03363HLA03598HLA03636HLA03650HLA03706HLA03707HLA03830HLA04019HLA04020HLA04258HLA04289HLA04290HLA04570HLA04731HLA04756HLA04852HLA05120HLA05130HLA05418HLA05574HLA05590HLA05754HLA05762HLA05873HLA06076HLA06163HLA06164HLA06165HLA06166HLA06305HLA06386HLA06405HLA06587HLA06656HLA06704HLA06731HLA07121HLA07213HLA07214HLA07349HLA07475HLA07476HLA07528HLA07556HLA07729HLA07941HLA07942HLA07943HLA08146HLA08177HLA08178HLA08307HLA09012HLA09111HLA09300HLA09669HLA09717HLA00404HLA00405HLA00406HLA01471HLA03081HLA03731HLA03826HLA04593HLA04616HLA04621HLA05210HLA05161HLA05567HLA05594HLA05606HLA06065HLA06710HLA06723HLA06736HLA07116HLA07237HLA08165HLA08210HLA08754HLA09202HLA00408HLA01344HLA01472HLA01673HLA01715HLA01739HLA01862HLA02120HLA02170HLA02240HLA02423HLA02430HLA02559HLA02593HLA03589HLA02764HLA02816HLA03024HLA03079HLA03252HLA03405HLA03539HLA03728HLA03739HLA03704HLA04699HLA06397HLA03705HLA05139HLA03801HLA04016HLA04277HLA04284HLA04764HLA04765HLA04823HLA04830HLA04845HLA05186HLA05189HLA05201HLA05311HLA05582HLA05584HLA05618HLA05733HLA05735HLA06124HLA06724HLA06898HLA07005HLA07020HLA07012HLA07117HLA07236HLA07360HLA07493HLA07944HLA07965HLA08118HLA08209HLA08211HLA08212HLA08213HLA08533HLA08755HLA08756HLA09035HLA09616HLA00410HLA01543HLA05731HLA09569HLA02800HLA04285HLA04287HLA04605HLA06126HLA06420HLA07730HLA09615HLA00411HLA00412HLA01355HLA01855HLA02567HLA03732HLA04264HLA04265HLA04270HLA04281HLA04288HLA05215HLA05607HLA06418HLA07024HLA07025HLA07377HLA07416HLA07954HLA09199HLA09726HLA00413HLA04253HLA00414HLA01820HLA02356HLA02522HLA02819HLA02820HLA04260HLA04261HLA04263HLA04267HLA04272HLA04278HLA04255HLA04589HLA04603HLA04622HLA04629HLA04736HLA06168HLA06400HLA06445HLA06728HLA07246HLA07348HLA07763HLA07952HLA07956HLA08166HLA08167HLA08539HLA08765HLA09039HLA09040HLA09042HLA09471HLA00415HLA00416HLA00417HLA00418HLA00419HLA01076HLA05788HLA05870HLA05882HLA06067HLA06074HLA06150HLA06167HLA06169HLA06310HLA06398HLA06399HLA06417HLA06419HLA06711HLA06712HLA06713HLA06726HLA07950HLA06727HLA06894HLA07006HLA01077HLA02375HLA07007HLA07008HLA07013HLA07014HLA07016HLA07021HLA07027HLA07029HLA07036HLA07118HLA01412HLA07119HLA07124HLA07140HLA07235HLA07238HLA07239HLA07240HLA07241HLA07315HLA07355HLA01425HLA07495HLA07496HLA07497HLA07498HLA07526HLA07537HLA07814HLA07940HLA07945HLA07946HLA01581HLA07947HLA07948HLA07949HLA07951HLA07953HLA07955HLA07957HLA08168HLA08175HLA08176HLA01660HLA08214HLA08215HLA08216HLA08217HLA08419HLA08477HLA08530HLA08537HLA08538HLA08540HLA01906HLA08545HLA08582HLA08764HLA08766HLA08767HLA08768HLA08812HLA08813HLA08814HLA08815HLA01925HLA08816HLA08817HLA08818HLA08954HLA09038HLA09041HLA09197HLA09198HLA09200HLA09201HLA02133HLA09330HLA09597HLA09624HLA09625HLA09626HLA09671HLA02346HLA02391HLA02414HLA02444HLA02467HLA02485HLA02526HLA02594HLA02599HLA02600HLA02617HLA02648HLA02681HLA02715HLA02729HLA02758HLA02817HLA02818HLA08536HLA02821HLA03048HLA02843HLA02881HLA07015HLA08169HLA02927HLA02993HLA02994HLA03544HLA02998HLA03027HLA02987HLA03163HLA03242HLA03362HLA03402HLA03723HLA03724HLA03725HLA03729HLA03733HLA03737HLA03687HLA03713HLA03827HLA03828HLA03835HLA04134HLA04256HLA04257HLA08206HLA04259HLA04262HLA04266HLA04268HLA04269HLA04271HLA04273HLA04274HLA04279HLA04280HLA04282HLA04283HLA04595HLA04618HLA04633HLA04702HLA04758HLA04777HLA04794HLA04822HLA05111HLA05122HLA05124HLA05162HLA05169HLA05171HLA05197HLA05202HLA05371HLA05396HLA05605HLA05613HLA05746HLA05747HLA05752HLA00420HLA01328HLA03572HLA05787HLA08080HLA00421HLA02086HLA02434HLA03226HLA03504HLA03734HLA03736HLA03802HLA03805HLA04254HLA04286HLA04590HLA04626HLA04574HLA04759HLA05165HLA05173HLA05183HLA05219HLA05403HLA05560HLA05569HLA05586HLA05599HLA05610HLA06402HLA06404HLA06446HLA06532HLA06533HLA06729HLA07022HLA07126HLA07242HLA07245HLA07502HLA07969HLA07973HLA08225HLA08226HLA08824HLA08826HLA08827HLA08831HLA09044HLA09048HLA09050HLA09205HLA09206HLA09207HLA09631HLA00423HLA09716HLA00424HLA01831HLA00425HLA00426HLA01078HLA01311HLA01451HLA01645HLA07030HLA07127HLA07120HLA07138HLA07142HLA07243HLA07359HLA07406HLA07499HLA07500HLA01711HLA07501HLA07529HLA07755HLA07970HLA07971HLA07972HLA07974HLA07975HLA08022HLA08119HLA01825HLA08171HLA08172HLA08173HLA08174HLA08221HLA08222HLA08224HLA08227HLA08413HLA08441HLA01851HLA08542HLA08543HLA08544HLA08822HLA08823HLA08825HLA08828HLA08829HLA08830HLA08832HLA01853HLA09043HLA09046HLA09047HLA09049HLA09076HLA09176HLA09502HLA09617HLA09628HLA09629HLA09630HLA09632HLA09728HLA01859HLA03106HLA05966HLA02193HLA02241HLA02429HLA02511HLA02525HLA02621HLA02622HLA02822HLA02824HLA02831HLA03007HLA03077HLA03122HLA03128HLA03214HLA03364HLA03404HLA03430HLA03437HLA03527HLA03678HLA03735HLA03699HLA03832HLA03992HLA04276HLA04298HLA04300HLA04301HLA04303HLA04309HLA04395HLA04610HLA04611HLA04617HLA04625HLA04695HLA04696HLA04763HLA04827HLA04838HLA04841HLA04842HLA04843HLA04851HLA05166HLA05167HLA08223HLA05170HLA05175HLA05191HLA05206HLA05218HLA05414HLA05543HLA05573HLA05592HLA05597HLA05604HLA05620HLA05739HLA05745HLA05763HLA05782HLA05883HLA05916HLA05947HLA06068HLA06385HLA06401HLA06403HLA06422HLA06436HLA06665HLA06730HLA06737HLA07009HLA07010HLA07244HLA07017HLA07018HLA07019HLA07023HLA09045HLA07026HLA00427HLA03586HLA01998HLA02292HLA03191HLA03978HLA04133HLA04293HLA04296HLA04305HLA04306HLA04391HLA04798HLA04800HLA05572HLA05880HLA06411HLA07011HLA07226HLA07976HLA07979HLA08156HLA08475HLA08532HLA08730HLA08732HLA09034HLA09609HLA01169HLA01174HLA08736HLA01602HLA01661HLA01832HLA01843HLA01856HLA07122HLA01907HLA02148HLA02397HLA02408HLA02586HLA02753HLA02785HLA02979HLA03212HLA07028HLA07031HLA03219HLA03438HLA03517HLA03531HLA07225HLA03563HLA03634HLA03681HLA04297HLA04302HLA04304HLA04308HLA08749HLA04310HLA04394HLA04587HLA04596HLA04608HLA04677HLA04701HLA04856HLA04799HLA04801HLA04802HLA04803HLA04832HLA05213HLA05310HLA08199HLA05382HLA05571HLA05585HLA05588HLA05593HLA05736HLA05852HLA06054HLA06125HLA06382HLA06383HLA06432HLA06431HLA06528HLA07222HLA06720HLA07052HLA07063HLA07075HLA07082HLA07108HLA09191HLA07109HLA07111HLA07134HLA07135HLA07224HLA07227HLA07228HLA07358HLA07487HLA07488HLA07977HLA07978HLA07980HLA07981HLA08155HLA08198HLA08200HLA08733HLA08734HLA08735HLA08737HLA09024HLA09025HLA09133HLA09189HLA09190HLA09192HLA09518HLA09646HLA09679HLA00430HLA02561HLA03018HLA04291HLA04292HLA05174HLA05176HLA05195HLA05602HLA05617HLA05783HLA06388HLA06406HLA06442HLA06707HLA06715HLA07066HLA07216HLA07357HLA07832HLA08154HLA08698HLA08699HLA08702HLA09016HLA09181HLA09725HLA00431HLA07492HLA00432HLA00991HLA01258HLA01301HLA01628HLA01681HLA01824HLA09515HLA09599HLA09601HLA01880HLA02178HLA02239HLA02708HLA02832HLA02833HLA02641HLA03429HLA03526HLA03624HLA03727HLA03682HLA03697HLA03754HLA04294HLA04295HLA04299HLA04307HLA04638HLA04697HLA04700HLA04745HLA04780HLA04828HLA04835HLA04837HLA04844HLA05164HLA05168HLA05184HLA05192HLA05207HLA05385HLA09180HLA05397HLA05423HLA05526HLA05559HLA05566HLA05576HLA05583HLA05598HLA05619HLA05734HLA08473HLA05737HLA05884HLA06043HLA06274HLA06275HLA06407HLA06440HLA06441HLA06714HLA06732HLA06734HLA07046HLA07065HLA07069HLA07073HLA07131HLA07478HLA07479HLA07480HLA07557HLA07733HLA07740HLA07815HLA08205HLA07826HLA07827HLA07830HLA07831HLA07833HLA07834HLA08098HLA08148HLA08149HLA08181HLA08182HLA08693HLA08695HLA08696HLA08697HLA08700HLA08701HLA09014HLA09015HLA09017HLA09179HLA09182HLA09473HLA00433HLA07937HLA00992HLA01865HLA02293HLA02422HLA02523HLA02611HLA03012HLA03015HLA04325HLA04340HLA04833HLA05587HLA05603HLA05626HLA05740HLA06390HLA06424HLA06534HLA06536HLA06718HLA07045HLA07074HLA07080HLA07845HLA07846HLA08054HLA08442HLA08709HLA08711HLA08713HLA09020HLA09022HLA09607HLA00434HLA01326HLA01902HLA07777HLA07778HLA03232HLA03459HLA03638HLA03759HLA03976HLA04314HLA04315HLA04317HLA04320HLA04344HLA04612HLA04630HLA04824HLA05159HLA05190HLA05564HLA05580HLA05627HLA05732HLA05784HLA05937HLA06042HLA06381HLA06447HLA06535HLA07047HLA07060HLA07061HLA07731HLA07828HLA07841HLA07844HLA08124HLA08194HLA08196HLA08721HLA08722HLA08727HLA09177HLA09186HLA09604HLA09608HLA00435HLA00436HLA01554HLA03538HLA05352HLA06444HLA06824HLA07272HLA08184HLA00437HLA00438HLA00439HLA00440HLA00441HLA00442HLA04974HLA04982HLA04983HLA04995HLA04996HLA05012HLA05013HLA05014HLA05015HLA05016HLA00443HLA05017HLA05022HLA05023HLA05024HLA05025HLA05026HLA05027HLA05028HLA05029HLA05030HLA00444HLA05031HLA05032HLA05033HLA05034HLA05035HLA05036HLA05064HLA05065HLA05066HLA05067HLA01079HLA05068HLA05069HLA05070HLA05071HLA05072HLA05073HLA05074HLA05075HLA05855HLA05076HLA05077HLA01080HLA05089HLA05090HLA07835HLA05079HLA05080HLA05081HLA05082HLA05083HLA05138HLA05221HLA05419HLA01408HLA05544HLA05554HLA05612HLA05764HLA05780HLA05820HLA05885HLA05886HLA05887HLA05888HLA01588HLA05889HLA05920HLA05996HLA06048HLA06069HLA06070HLA06071HLA06127HLA06170HLA06171HLA06277HLA06306HLA06387HLA06389HLA06391HLA06392HLA06408HLA06409HLA06410HLA06423HLA01662HLA08720HLA01672HLA06425HLA06429HLA06430HLA06437HLA06449HLA06525HLA06655HLA06662HLA06705HLA06706HLA01720HLA06716HLA06717HLA06719HLA06733HLA06735HLA06828HLA06896HLA06902HLA07051HLA07057HLA08183HLA01729HLA07058HLA07059HLA07070HLA07071HLA07072HLA07078HLA07079HLA07081HLA07320HLA07130HLA01833HLA07132HLA07133HLA07182HLA07215HLA07217HLA07218HLA07219HLA07220HLA07221HLA07316HLA01844HLA07373HLA07474HLA07477HLA07481HLA07482HLA07483HLA07484HLA07486HLA07822HLA07734HLA01863HLA07735HLA07736HLA07737HLA07738HLA07739HLA07756HLA07829HLA07836HLA07837HLA07838HLA01864HLA07839HLA07840HLA07842HLA07843HLA07930HLA08126HLA08147HLA08150HLA08151HLA08152HLA01877HLA08153HLA08179HLA08180HLA08185HLA08186HLA08187HLA08188HLA08189HLA08190HLA08191HLA01889HLA08192HLA08193HLA08195HLA08197HLA08402HLA08418HLA08474HLA08478HLA08526HLA08527HLA08528HLA08688HLA08689HLA08691HLA08692HLA08703HLA08704HLA08705HLA08706HLA08707HLA01908HLA03107HLA01961HLA08708HLA08710HLA08712HLA08714HLA08715HLA08716HLA08717HLA08718HLA08719HLA08723HLA02010HLA08724HLA08725HLA08726HLA08833HLA08897HLA09013HLA09018HLA09019HLA09021HLA02139HLA09136HLA09178HLA09183HLA09184HLA09185HLA09187HLA09188HLA09451HLA09511HLA09598HLA09602HLA09603HLA09605HLA09606HLA09689HLA09831HLA02205HLA08529HLA02354HLA02380HLA02425HLA02448HLA02459HLA02475HLA07485HLA02564HLA02598HLA02614HLA02680HLA02697HLA02709HLA02730HLA02789HLA02834HLA02835HLA02943HLA03004HLA03013HLA03135HLA03139HLA03239HLA03298HLA03310HLA03753HLA03365HLA03414HLA03419HLA03436HLA03439HLA03444HLA03477HLA03515HLA03546HLA03631HLA03623HLA03698HLA03700HLA03701HLA03702HLA03703HLA03819HLA03977HLA04021HLA04130HLA04318HLA04322HLA04323HLA04324HLA04328HLA04329HLA04330HLA04331HLA04335HLA04338HLA04339HLA04342HLA04343HLA04347HLA04348HLA04396HLA04399HLA04588HLA04594HLA04597HLA08762HLA04601HLA04607HLA04609HLA00445HLA01586HLA05786HLA06172HLA06644HLA08157HLA08158HLA08159HLA08963HLA09834HLA00446HLA04345HLA04392HLA05309HLA05591HLA06413HLA07273HLA08753HLA09026HLA09194HLA00447HLA03758HLA00448HLA07521HLA08740HLA00449HLA00450HLA01136HLA01238HLA01322HLA01835HLA01857HLA01879HLA02302HLA02445HLA03017HLA06138HLA03280HLA07742HLA03420HLA03440HLA03482HLA03632HLA03626HLA03680HLA03696HLA03763HLA03767HLA03818HLA03975HLA04319HLA04332HLA04393HLA04583HLA05180HLA05188HLA07053HLA08201HLA05196HLA05395HLA05416HLA05579HLA05616HLA05753HLA05785HLA05790HLA05863HLA05874HLA05890HLA06072HLA06173HLA06393HLA06394HLA06412HLA06428HLA06721HLA06814HLA07050HLA07110HLA07345HLA07363HLA07489HLA07530HLA07531HLA07743HLA07847HLA07938HLA08088HLA08400HLA08427HLA08728HLA08729HLA08731HLA08738HLA08739HLA08741HLA09610HLA09023HLA09051HLA09165HLA09166HLA09193HLA09683HLA00453HLA00454HLA01145HLA04620HLA04858HLA05178HLA07137HLA07555HLA07785HLA00455HLA02766HLA01315HLA01885HLA02428HLA03127HLA03285HLA04326HLA04337HLA04600HLA04836HLA04840HLA05172HLA05565HLA05623HLA06001HLA06415HLA07064HLA07123HLA07230HLA07318HLA07853HLA07855HLA08535HLA08742HLA08752HLA00456HLA00457HLA00458HLA00459HLA01138HLA01413HLA01705HLA01787HLA04679HLA01799HLA01878HLA01954HLA01935HLA03619HLA01969HLA02304HLA02357HLA02527HLA07783HLA02605HLA02791HLA02842HLA03760HLA03988HLA04129HLA04313HLA04316HLA04334HLA04336HLA04591HLA04592HLA04602HLA04757HLA04766HLA04825HLA04834HLA05185HLA05187HLA05199HLA05203HLA05204HLA05205HLA05212HLA05214HLA05394HLA05570HLA05575HLA05595HLA05608HLA05751HLA05837HLA06136HLA06384HLA06396HLA06414HLA06421HLA06426HLA06439HLA06582HLA06722HLA06897HLA07055HLA07062HLA07076HLA07083HLA07231HLA07114HLA07223HLA07232HLA07490HLA07491HLA07741HLA07745HLA07782HLA07784HLA07786HLA07810HLA07852HLA07854HLA07856HLA08160HLA08202HLA08218HLA08399HLA08421HLA08426HLA08744HLA08745HLA08746HLA08747HLA08748HLA08751HLA08893HLA09029HLA09086HLA09196HLA09299HLA09611HLA09613HLA09614HLA00462HLA00463HLA01721HLA02207HLA05194HLA05748HLA06174HLA07141HLA07274HLA07541HLA07859HLA09727HLA00464HLA00465HLA01469HLA02087HLA02253HLA02427HLA03121HLA03415HLA03455HLA03820HLA04327HLA04341HLA04619HLA04694HLA04778HLA04784HLA04826HLA05119HLA05415HLA05749HLA05789HLA05891HLA07858HLA05892HLA05921HLA06128HLA06147HLA06175HLA06435HLA06529HLA07125HLA07128HLA07129HLA07527HLA07540HLA07804HLA07824HLA07825HLA07860HLA07861HLA08219HLA08220HLA08304HLA08428HLA08541HLA08819HLA08820HLA08821HLA09203HLA09204HLA09820HLA00467HLA01081HLA02424HLA03146HLA04624HLA05200HLA05893HLA07760HLA07789HLA07791HLA08757HLA08758HLA08759HLA08760HLA08763HLA09620HLA00468HLA00469HLA00470HLA00471HLA01803HLA01909HLA05220HLA06416HLA08476HLA09036HLA09627HLA00472HLA04779HLA05865HLA00473HLA00474HLA01124HLA01342HLA03108HLA01424HLA01884HLA02022HLA02396HLA02404HLA02438HLA02836HLA02837HLA02928HLA03813HLA04312HLA04598HLA04579HLA04639HLA04693HLA04831HLA05113HLA05115HLA05158HLA05160HLA05181HLA05198HLA05216HLA05558HLA05581HLA05600HLA05614HLA05615HLA05625HLA05750HLA05755HLA05854HLA05879HLA06002HLA06073HLA06123HLA06434HLA06524HLA06725HLA07049HLA07056HLA07067HLA07077HLA07139HLA07494HLA07787HLA07788HLA07790HLA08170HLA08534HLA08694HLA08761HLA08808HLA09037HLA09618HLA09619HLA09621HLA09622HLA09623HLA00475HLA02041HLA02868HLA04627HLA05596HLA06303HLA07136HLA08117HLA08161HLA08204HLA08743HLA09027HLA09028HLA00476HLA04604HLA04829HLA04839HLA05624HLA06047HLA06438HLA07048HLA07234HLA00478HLA01708HLA02242HLA06276HLA02303HLA02686HLA03115HLA03238HLA03425HLA03726HLA03738HLA04321HLA05871HLA04333HLA04346HLA04599HLA04632HLA04698HLA04767HLA05163HLA05179HLA05182HLA05208HLA05217HLA05521HLA05577HLA05578HLA05589HLA05621HLA05738HLA06395HLA06433HLA06448HLA06450HLA06708HLA06778HLA06890HLA09822HLA07054HLA07113HLA07112HLA07229HLA07317HLA07744HLA07848HLA07849HLA07850HLA07851HLA08162HLA08163HLA08203HLA08811HLA08892HLA08932HLA09115HLA09195HLA09503HLA09612HLA00481HLA04311HLA04628HLA04631HLA05177HLA05568HLA06709HLA07115HLA08164HLA08208HLA00482HLA00993HLA02319HLA03545HLA04623HLA05211HLA05609HLA06427HLA07068HLA07233HLA07857HLA08207HLA08531HLA08750HLA09030HLA09031HLA09032HLA09033HLA00483HLA00484HLA02839HLA05601HLA06443HLA08690HLA09600HLA00934HLA02225HLA02450HLA00936HLA02226HLA00937HLA05913HLA01339HLA02224HLA07813HLA09519HLA09694HLA00938_HLA00936HLA00938_HLA02226HLA00938_HLA00937HLA00938_HLA05913HLA00938_HLA02224HLA00938_HLA07813HLA00938_HLA09519HLA00938_HLA09694HLA01096HLA02280HLA02263HLA02271HLA02274HLA02266HLA02269HLA02647HLA01755HLA02265HLA02273HLA02279HLA02264HLA05914HLA02275HLA02270HLA02277HLA02278HLA02267HLA02276HLA02268HLA02272HLA00939HLA02283HLA02288HLA02281HLA02282HLA03588HLA00940HLA02285HLA00941HLA03807HLA07532HLA00942HLA00943HLA00944HLA00945HLA00946HLA02284HLA02954HLA02972HLA02973HLA03159HLA03553HLA03552HLA03556HLA03557HLA03558HLA04419HLA07536HLA00947HLA00948HLA06452HLA00949HLA00950HLA00951HLA02287HLA03555HLA00952HLA01357HLA02286HLA02876HLA02969HLA03192HLA03193HLA03396HLA03397HLA03398HLA03399HLA03400HLA04000HLA08306HLA02546HLA02557HLA02548HLA02551HLA02547HLA02549HLA02556HLA02550HLA02552HLA02554HLA02555HLA02553HLA02626HLA02629HLA02653HLA02630HLA02634HLA02632HLA02628HLA02631HLA02627HLA02654HLA02658HLA02657HLA02659HLA02656HLA02660HLA02655HLA02662HLA02663HLA02661HLA02664HLA02801HLA02802HLA02803 \ No newline at end of file diff --git a/data/indices/yara/hla_reference_rna.rid.limits b/data/indices/yara/hla_reference_rna.rid.limits deleted file mode 100644 index 656df9e..0000000 Binary files a/data/indices/yara/hla_reference_rna.rid.limits and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.sa.ind b/data/indices/yara/hla_reference_rna.sa.ind deleted file mode 100644 index 56e79c3..0000000 Binary files a/data/indices/yara/hla_reference_rna.sa.ind and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.sa.len b/data/indices/yara/hla_reference_rna.sa.len deleted file mode 100644 index ac440f9..0000000 Binary files a/data/indices/yara/hla_reference_rna.sa.len and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.sa.val b/data/indices/yara/hla_reference_rna.sa.val deleted file mode 100644 index d73f368..0000000 Binary files a/data/indices/yara/hla_reference_rna.sa.val and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.txt.concat b/data/indices/yara/hla_reference_rna.txt.concat deleted file mode 100644 index 66f37d2..0000000 Binary files a/data/indices/yara/hla_reference_rna.txt.concat and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.txt.limits b/data/indices/yara/hla_reference_rna.txt.limits deleted file mode 100644 index 8602c87..0000000 Binary files a/data/indices/yara/hla_reference_rna.txt.limits and /dev/null differ diff --git a/data/indices/yara/hla_reference_rna.txt.size b/data/indices/yara/hla_reference_rna.txt.size deleted file mode 100644 index 692b67f..0000000 Binary files a/data/indices/yara/hla_reference_rna.txt.size and /dev/null differ diff --git a/docs/README.md b/docs/README.md index bec6422..851509e 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,9 +2,9 @@ The nf-core/hlatyping documentation is split into the following pages: -* [Usage](usage.md) - * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. -* [Output](output.md) - * An overview of the different results produced by the pipeline and how to interpret them. +- [Usage](usage.md) + - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. +- [Output](output.md) + - An overview of the different results produced by the pipeline and how to interpret them. You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png new file mode 100755 index 0000000..361d0e4 Binary files /dev/null and b/docs/images/mqc_fastqc_adapter.png differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png new file mode 100755 index 0000000..cb39ebb Binary files /dev/null and b/docs/images/mqc_fastqc_counts.png differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png new file mode 100755 index 0000000..a4b89bf Binary files /dev/null and b/docs/images/mqc_fastqc_quality.png differ diff --git a/docs/images/nf-core-hlatyping_logo.png b/docs/images/nf-core-hlatyping_logo.png deleted file mode 100644 index e1538bb..0000000 Binary files a/docs/images/nf-core-hlatyping_logo.png and /dev/null differ diff --git a/docs/images/nf-core-hlatyping_logo_dark.png b/docs/images/nf-core-hlatyping_logo_dark.png new file mode 100644 index 0000000..736d468 Binary files /dev/null and b/docs/images/nf-core-hlatyping_logo_dark.png differ diff --git a/docs/images/nf-core-hlatyping_logo_light.png b/docs/images/nf-core-hlatyping_logo_light.png new file mode 100644 index 0000000..578fd90 Binary files /dev/null and b/docs/images/nf-core-hlatyping_logo_light.png differ diff --git a/docs/output.md b/docs/output.md index 410b360..8d3f318 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,17 +1,40 @@ # nf-core/hlatyping: Output +## Introduction + This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. ## Pipeline overview -The pipeline is built using [Nextflow](https://www.nextflow.io/) -and processes data using the following steps: +The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: + +- [FastQC](#fastqc) - Raw read QC +- [OptiType](#optitype) - HLA genotyping based on integer linear programming +- [MultiQC](#multiqc) - Aggregate report describing results from the whole pipeline +- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution + +### FastQC + +
+Output files + +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + +
+ +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -* [OptiType](#optitype) - HLA genotyping based on integer linear programming -* [MultiQC](#multiqc) - Aggregate report describing results from the whole pipeline -* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) + +![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) + +![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) + +> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. ## OptiType @@ -31,33 +54,37 @@ Additionally, a coverage plot of the predicted HLA genotype is produced for qual **Output directory: `results/{timestamp}`** -* `{prefix}_{timestamp}_result.tsv` - * TSV file, containing the predicted optimal (anf if enumerated, sub-optimal) HLA genotype -* `{prefix}_{timestamp}_coverage_plot.pdf` - * pdf file, containing a coverage plot of the predicted alleles +- `{prefix}_{timestamp}_result.tsv` + - TSV file, containing the predicted optimal (anf if enumerated, sub-optimal) HLA genotype +- `{prefix}_{timestamp}_coverage_plot.pdf` + - pdf file, containing a coverage plot of the predicted alleles -## MultiQC +### MultiQC -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. +
+Output files -The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. +- `multiqc/` + - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + - `multiqc_plots/`: directory containing static images from the report in various formats. -For more information about how to use MultiQC reports, see [https://multiqc.info](https://multiqc.info). +
-**Output files:** +[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -* `multiqc/` - * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - * `multiqc_plots/`: directory containing static images from the report in various formats. +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . -## Pipeline information +### Pipeline information -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +
+Output files + +- `pipeline_info/` + - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. + - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. -**Output files:** +
-* `pipeline_info/` - * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`. - * Documentation for interpretation of results in HTML format: `results_description.html`. +[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md index deaae4e..60aa3ae 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,13 +1,85 @@ # nf-core/hlatyping: Usage +## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hlatyping/usage](https://nf-co.re/hlatyping/usage) + +> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ + ## Introduction +The `hlatyping` pipeline can currently deal with two input formats: `.fastq{.gz}` or `.bam`. If the input file type is `bam`, than the pipeline extracts all reads from it and performs an mapping additional step with the `yara` mapper against the HLA reference sequence. Indices are generated using `yara`. OptiType uses [razers3](https://github.com/seqan/seqan/tree/master/apps/razers3), which is very memory consuming. In order to avoid memory issues during pipeline execution, we reduce the mapping information on the relevant HLA regions on chromosome 6. + +### DAG with `.fastq{.gz}` as input + +Creates a config file from the command line arguments, which is then passed to OptiType. In parallel, the fastqs are unzipped if they are passed as archives. OptiType is then used for the HLA typing. + +![DAG with `fastq.{gz}` files](images/hlatyping_dag_fastq.png) + +### DAG with `.bam` as input + +Creates a config file from the command line arguments, which is then passed to OptiType. In parallel, the reads are extracted from the bam file and mapped again against the HLA reference sequence on chromosome 6. OptiType is then used for the HLA typing. + +![DAG with `.bam` file](images/hlatyping_dag_bam.png) + +## Samplesheet input + +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. + +```bash +--input '[path to samplesheet file]' +``` + +### Multiple runs + +The `sample` identifiers have to be specified with the `fastq` files and the sequencing type: + +```console +sample,fastq_1,fastq_2,seq_type +CONTROL_PE,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,dna +CONTROL_SE,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,dna +``` + +### Full samplesheet + +The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below. + +A final samplesheet file consisting of both single- and paired-end data may look something like the one below. + +```console +sample,fastq_1,fastq_2,seq_type +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,dna +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,dna +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,dna +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,dna +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,dna +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,dna +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,dna +``` + +The pipeline can also process `BAM` files. If you want to process a `BAM` file, just add the corresponding column to the samplesheet and provide the full path to the file. `FASTQ` and `BAM` files can be mixed in the same sample sheet. + +```console +sample,fastq_1,fastq_2,bam,seq_type +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,,dna +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,,rna +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.bam,,dna +``` + +| Column | Description | +| ---------- | -------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `bam` | OPTIONAL. Full path to BAM file. | +| `seq_type` | `DNA` or `RNA`. | + +An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. + ## Running the pipeline The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/hlatyping --input '*_R{1,2}.fastq.gz' -profile docker +nextflow run nf-core/hlatyping --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -15,15 +87,15 @@ This will launch the pipeline with the `docker` configuration profile. See below Note that the pipeline will create the following files in your working directory: ```bash -work # Directory containing the nextflow working files -results # Finished results (configurable, see below) -.nextflow_log # Log file from Nextflow +work # Directory containing the nextflow working files + # Finished results in specified location (defined with --outdir) +.nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` ### HLA references -The **nf-core/hlatyping** pipeline uses a default HLA reference which is located in the pipelines root directory in `./data/references` and the corresponding mapper indices in `./data/indices/yara`. The references are based on the IMGT/HLA Release 3.14.0, July 2013, and have been processed as described in the [publication](https://doi.org/10.1093/bioinformatics/btu548) of OptiType. +The **nf-core/hlatyping** pipeline uses a default HLA reference which is located in the pipelines root directory in `./data/references`. The references are based on the IMGT/HLA Release `3.14.0`, July 2013, and have been processed as described in the [publication](https://doi.org/10.1093/bioinformatics/btu548) of OptiType. The reference is automatically set during the pipeline execution based on the information provided in the `seq_type` column of the samplesheet (`dna` or `rna`). You can always download new versions from the [HLA database](https://www.ebi.ac.uk/ipd/imgt/hla/docs/release.html), but be aware that these allele sets are missing intron sequence information, which will have a negative influence in the HLA typing outcome in case of DNAseq. @@ -39,7 +111,7 @@ nextflow pull nf-core/hlatyping ### Reproducibility -It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the nf-core/hlatyping releases page and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. @@ -53,7 +125,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/). > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -64,23 +136,25 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles. If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. -* `docker` - * A generic configuration profile to be used with [Docker](https://docker.com/) - * Pulls software from Docker Hub: [`nfcore/hlatyping`](https://hub.docker.com/r/nfcore/hlatyping/) -* `singularity` - * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) - * Pulls software from Docker Hub: [`nfcore/hlatyping`](https://hub.docker.com/r/nfcore/hlatyping/) -* `conda` - * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker or Singularity. - * A generic configuration profile to be used with [Conda](https://conda.io/docs/) - * Pulls most software from [Bioconda](https://bioconda.github.io/) -* `test` - * A profile with a complete configuration for automated testing - * Includes links to test data so needs no other parameters +- `docker` + - A generic configuration profile to be used with [Docker](https://docker.com/) +- `singularity` + - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) +- `podman` + - A generic configuration profile to be used with [Podman](https://podman.io/) +- `shifter` + - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) +- `charliecloud` + - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `conda` + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters ### `-resume` -Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. +Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names. @@ -88,27 +162,120 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information. -#### Custom resource requests +## Custom configuration + +### Resource requests + +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. + +For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: + +```console +[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) +Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' + +Caused by: + Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) + +Command executed: + STAR \ + --genomeDir star \ + --readFilesIn WT_REP1_trimmed.fq.gz \ + --runThreadN 2 \ + --outFileNamePrefix WT_REP1. \ + -Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped. +Command exit status: + 137 -Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config: +Command output: + (empty) + +Command error: + .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. +Work dir: + /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb + +Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` +``` + +To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). +We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`. +If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). +The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. +The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. +Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. +The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. ```nextflow process { - withName: star { - memory = 32.GB - } + withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { + memory = 100.GB + } } ``` -See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information. +> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. +> +> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. + +### Updating containers + +The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. -If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. +1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) +2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) +3. Create the custom config accordingly: + + - For Docker: + + ```nextflow + process { + withName: PANGOLIN { + container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Singularity: + + ```nextflow + process { + withName: PANGOLIN { + container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Conda: + + ```nextflow + process { + withName: PANGOLIN { + conda = 'bioconda::pangolin=3.0.5' + } + } + ``` + +> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. + +### nf-core/configs + +In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. + +See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files. If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -### Running in the background +## Azure Resource Requests + +To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. +We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. + +Note that the choice of VM size depends on your quota and the overall workload during the analysis. +For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). + +## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. @@ -117,7 +284,7 @@ The Nextflow `-bg` flag launches Nextflow in the background, detached from your Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time. Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs). -#### Nextflow memory requirements +## Nextflow memory requirements In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 630d5c1..0000000 --- a/environment.yml +++ /dev/null @@ -1,18 +0,0 @@ -# You can use this file to create a conda environment for this pipeline: -# conda env create -f environment.yml -name: nf-core-hlatyping-1.2.0 -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - conda-forge::coincbc=2.9.9 - - conda-forge::libiconv=1.15 - - conda-forge::python=3.6.10 - - conda-forge::markdown=3.1.1 - - conda-forge::pymdown-extensions=6.0 - - conda-forge::pygments=2.5.2 - - bioconda::multiqc=1.9 - - bioconda::optitype=1.3.4 - - bioconda::yara=1.0.2 - - bioconda::samtools=1.9 \ No newline at end of file diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy new file mode 100755 index 0000000..b3d092f --- /dev/null +++ b/lib/NfcoreSchema.groovy @@ -0,0 +1,529 @@ +// +// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. +// + +import org.everit.json.schema.Schema +import org.everit.json.schema.loader.SchemaLoader +import org.everit.json.schema.ValidationException +import org.json.JSONObject +import org.json.JSONTokener +import org.json.JSONArray +import groovy.json.JsonSlurper +import groovy.json.JsonBuilder + +class NfcoreSchema { + + // + // Resolve Schema path relative to main workflow directory + // + public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { + return "${workflow.projectDir}/${schema_filename}" + } + + // + // Function to loop over all parameters defined in schema and check + // whether the given parameters adhere to the specifications + // + /* groovylint-disable-next-line UnusedPrivateMethodParameter */ + public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { + def has_error = false + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// + // Check for nextflow core params and unexpected params + def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text + def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') + def nf_params = [ + // Options for base `nextflow` command + 'bg', + 'c', + 'C', + 'config', + 'd', + 'D', + 'dockerize', + 'h', + 'log', + 'q', + 'quiet', + 'syslog', + 'v', + 'version', + + // Options for `nextflow run` command + 'ansi', + 'ansi-log', + 'bg', + 'bucket-dir', + 'c', + 'cache', + 'config', + 'dsl2', + 'dump-channels', + 'dump-hashes', + 'E', + 'entry', + 'latest', + 'lib', + 'main-script', + 'N', + 'name', + 'offline', + 'params-file', + 'pi', + 'plugins', + 'poll-interval', + 'pool-size', + 'profile', + 'ps', + 'qs', + 'queue-size', + 'r', + 'resume', + 'revision', + 'stdin', + 'stub', + 'stub-run', + 'test', + 'w', + 'with-charliecloud', + 'with-conda', + 'with-dag', + 'with-docker', + 'with-mpi', + 'with-notification', + 'with-podman', + 'with-report', + 'with-singularity', + 'with-timeline', + 'with-tower', + 'with-trace', + 'with-weblog', + 'without-docker', + 'without-podman', + 'work-dir' + ] + def unexpectedParams = [] + + // Collect expected parameters from the schema + def expectedParams = [] + def enums = [:] + for (group in schemaParams) { + for (p in group.value['properties']) { + expectedParams.push(p.key) + if (group.value['properties'][p.key].containsKey('enum')) { + enums[p.key] = group.value['properties'][p.key]['enum'] + } + } + } + + for (specifiedParam in params.keySet()) { + // nextflow params + if (nf_params.contains(specifiedParam)) { + log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" + has_error = true + } + // unexpected params + def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' + def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } + def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() + def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) + if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { + // Temporarily remove camelCase/camel-case params #1035 + def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} + if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ + unexpectedParams.push(specifiedParam) + } + } + } + + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// + // Validate parameters against the schema + InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() + JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) + + // Remove anything that's in params.schema_ignore_params + raw_schema = removeIgnoredParams(raw_schema, params) + + Schema schema = SchemaLoader.load(raw_schema) + + // Clean the parameters + def cleanedParams = cleanParameters(params) + + // Convert to JSONObject + def jsonParams = new JsonBuilder(cleanedParams) + JSONObject params_json = new JSONObject(jsonParams.toString()) + + // Validate + try { + schema.validate(params_json) + } catch (ValidationException e) { + println '' + log.error 'ERROR: Validation of pipeline parameters failed!' + JSONObject exceptionJSON = e.toJSON() + printExceptions(exceptionJSON, params_json, log, enums) + println '' + has_error = true + } + + // Check for unexpected parameters + if (unexpectedParams.size() > 0) { + Map colors = NfcoreTemplate.logColours(params.monochrome_logs) + println '' + def warn_msg = 'Found unexpected parameters:' + for (unexpectedParam in unexpectedParams) { + warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" + } + log.warn warn_msg + log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" + println '' + } + + if (has_error) { + System.exit(1) + } + } + + // + // Beautify parameters for --help + // + public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { + Map colors = NfcoreTemplate.logColours(params.monochrome_logs) + Integer num_hidden = 0 + String output = '' + output += 'Typical pipeline command:\n\n' + output += " ${colors.cyan}${command}${colors.reset}\n\n" + Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) + Integer max_chars = paramsMaxChars(params_map) + 1 + Integer desc_indent = max_chars + 14 + Integer dec_linewidth = 160 - desc_indent + for (group in params_map.keySet()) { + Integer num_params = 0 + String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (group_params.get(param).hidden && !params.show_hidden_params) { + num_hidden += 1 + continue; + } + def type = '[' + group_params.get(param).type + ']' + def description = group_params.get(param).description + def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' + def description_default = description + colors.dim + defaultValue + colors.reset + // Wrap long description texts + // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap + if (description_default.length() > dec_linewidth){ + List olines = [] + String oline = "" // " " * indent + description_default.split(" ").each() { wrd -> + if ((oline.size() + wrd.size()) <= dec_linewidth) { + oline += wrd + " " + } else { + olines += oline + oline = wrd + " " + } + } + olines += oline + description_default = olines.join("\n" + " " * desc_indent) + } + group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' + num_params += 1 + } + group_output += '\n' + if (num_params > 0){ + output += group_output + } + } + if (num_hidden > 0){ + output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset + } + output += NfcoreTemplate.dashedLine(params.monochrome_logs) + return output + } + + // + // Groovy Map summarising parameters/workflow options used by the pipeline + // + public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { + // Get a selection of core Nextflow workflow options + def Map workflow_summary = [:] + if (workflow.revision) { + workflow_summary['revision'] = workflow.revision + } + workflow_summary['runName'] = workflow.runName + if (workflow.containerEngine) { + workflow_summary['containerEngine'] = workflow.containerEngine + } + if (workflow.container) { + workflow_summary['container'] = workflow.container + } + workflow_summary['launchDir'] = workflow.launchDir + workflow_summary['workDir'] = workflow.workDir + workflow_summary['projectDir'] = workflow.projectDir + workflow_summary['userName'] = workflow.userName + workflow_summary['profile'] = workflow.profile + workflow_summary['configFiles'] = workflow.configFiles.join(', ') + + // Get pipeline parameters defined in JSON Schema + def Map params_summary = [:] + def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) + for (group in params_map.keySet()) { + def sub_params = new LinkedHashMap() + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (params.containsKey(param)) { + def params_value = params.get(param) + def schema_value = group_params.get(param).default + def param_type = group_params.get(param).type + if (schema_value != null) { + if (param_type == 'string') { + if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { + def sub_string = schema_value.replace('\$projectDir', '') + sub_string = sub_string.replace('\${projectDir}', '') + if (params_value.contains(sub_string)) { + schema_value = params_value + } + } + if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { + def sub_string = schema_value.replace('\$params.outdir', '') + sub_string = sub_string.replace('\${params.outdir}', '') + if ("${params.outdir}${sub_string}" == params_value) { + schema_value = params_value + } + } + } + } + + // We have a default in the schema, and this isn't it + if (schema_value != null && params_value != schema_value) { + sub_params.put(param, params_value) + } + // No default in the schema, and this isn't empty + else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { + sub_params.put(param, params_value) + } + } + } + params_summary.put(group, sub_params) + } + return [ 'Core Nextflow options' : workflow_summary ] << params_summary + } + + // + // Beautify parameters for summary and return as string + // + public static String paramsSummaryLog(workflow, params) { + Map colors = NfcoreTemplate.logColours(params.monochrome_logs) + String output = '' + def params_map = paramsSummaryMap(workflow, params) + def max_chars = paramsMaxChars(params_map) + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + if (group_params) { + output += colors.bold + group + colors.reset + '\n' + for (param in group_params.keySet()) { + output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' + } + output += '\n' + } + } + output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" + output += NfcoreTemplate.dashedLine(params.monochrome_logs) + return output + } + + // + // Loop over nested exceptions and print the causingException + // + private static void printExceptions(ex_json, params_json, log, enums, limit=5) { + def causingExceptions = ex_json['causingExceptions'] + if (causingExceptions.length() == 0) { + def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ + // Missing required param + if (m.matches()) { + log.error "* Missing required parameter: --${m[0][1]}" + } + // Other base-level error + else if (ex_json['pointerToViolation'] == '#') { + log.error "* ${ex_json['message']}" + } + // Error with specific param + else { + def param = ex_json['pointerToViolation'] - ~/^#\// + def param_val = params_json[param].toString() + if (enums.containsKey(param)) { + def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" + if (enums[param].size() > limit) { + log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" + } else { + log.error "${error_msg}: ${enums[param].join(', ')})" + } + } else { + log.error "* --${param}: ${ex_json['message']} (${param_val})" + } + } + } + for (ex in causingExceptions) { + printExceptions(ex, params_json, log, enums) + } + } + + // + // Remove an element from a JSONArray + // + private static JSONArray removeElement(json_array, element) { + def list = [] + int len = json_array.length() + for (int i=0;i + if(raw_schema.keySet().contains('definitions')){ + raw_schema.definitions.each { definition -> + for (key in definition.keySet()){ + if (definition[key].get("properties").keySet().contains(ignore_param)){ + // Remove the param to ignore + definition[key].get("properties").remove(ignore_param) + // If the param was required, change this + if (definition[key].has("required")) { + def cleaned_required = removeElement(definition[key].required, ignore_param) + definition[key].put("required", cleaned_required) + } + } + } + } + } + if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { + raw_schema.get("properties").remove(ignore_param) + } + if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { + def cleaned_required = removeElement(raw_schema.required, ignore_param) + raw_schema.put("required", cleaned_required) + } + } + return raw_schema + } + + // + // Clean and check parameters relative to Nextflow native classes + // + private static Map cleanParameters(params) { + def new_params = params.getClass().newInstance(params) + for (p in params) { + // remove anything evaluating to false + if (!p['value']) { + new_params.remove(p.key) + } + // Cast MemoryUnit to String + if (p['value'].getClass() == nextflow.util.MemoryUnit) { + new_params.replace(p.key, p['value'].toString()) + } + // Cast Duration to String + if (p['value'].getClass() == nextflow.util.Duration) { + new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) + } + // Cast LinkedHashMap to String + if (p['value'].getClass() == LinkedHashMap) { + new_params.replace(p.key, p['value'].toString()) + } + } + return new_params + } + + // + // This function tries to read a JSON params file + // + private static LinkedHashMap paramsLoad(String json_schema) { + def params_map = new LinkedHashMap() + try { + params_map = paramsRead(json_schema) + } catch (Exception e) { + println "Could not read parameters settings from JSON. $e" + params_map = new LinkedHashMap() + } + return params_map + } + + // + // Method to actually read in JSON file using Groovy. + // Group (as Key), values are all parameters + // - Parameter1 as Key, Description as Value + // - Parameter2 as Key, Description as Value + // .... + // Group + // - + private static LinkedHashMap paramsRead(String json_schema) throws Exception { + def json = new File(json_schema).text + def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') + def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') + /* Tree looks like this in nf-core schema + * definitions <- this is what the first get('definitions') gets us + group 1 + title + description + properties + parameter 1 + type + description + parameter 2 + type + description + group 2 + title + description + properties + parameter 1 + type + description + * properties <- parameters can also be ungrouped, outside of definitions + parameter 1 + type + description + */ + + // Grouped params + def params_map = new LinkedHashMap() + schema_definitions.each { key, val -> + def Map group = schema_definitions."$key".properties // Gets the property object of the group + def title = schema_definitions."$key".title + def sub_params = new LinkedHashMap() + group.each { innerkey, value -> + sub_params.put(innerkey, value) + } + params_map.put(title, sub_params) + } + + // Ungrouped params + def ungrouped_params = new LinkedHashMap() + schema_properties.each { innerkey, value -> + ungrouped_params.put(innerkey, value) + } + params_map.put("Other parameters", ungrouped_params) + + return params_map + } + + // + // Get maximum number of characters across all parameter names + // + private static Integer paramsMaxChars(params_map) { + Integer max_chars = 0 + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (param.size() > max_chars) { + max_chars = param.size() + } + } + } + return max_chars + } +} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy new file mode 100755 index 0000000..27feb00 --- /dev/null +++ b/lib/NfcoreTemplate.groovy @@ -0,0 +1,313 @@ +// +// This file holds several functions used within the nf-core pipeline template. +// + +import org.yaml.snakeyaml.Yaml + +class NfcoreTemplate { + + // + // Check AWS Batch related parameters have been specified correctly + // + public static void awsBatch(workflow, params) { + if (workflow.profile.contains('awsbatch')) { + // Check params.awsqueue and params.awsregion have been set if running on AWSBatch + assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" + // Check outdir paths to be S3 buckets if running on AWSBatch + assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" + } + } + + // + // Warn if a -profile or Nextflow config has not been provided to run the pipeline + // + public static void checkConfigProvided(workflow, log) { + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + } + } + + // + // Construct and send completion email + // + public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = workflow.manifest.version + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + + // Check if we are only sending emails on failure + def email_address = params.email + if (!params.email && params.email_on_fail && !workflow.success) { + email_address = params.email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("$projectDir/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("$projectDir/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("$projectDir/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(params.monochrome_logs) + if (email_address) { + try { + if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + mail_cmd += [ '-A', mqc_report ] + } + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_d = new File("${params.outdir}/pipeline_info/") + if (!output_d.exists()) { + output_d.mkdirs() + } + def output_hf = new File(output_d, "pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + def output_tf = new File(output_d, "pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + } + + // + // Construct and send adaptive card + // https://adaptivecards.io + // + public static void adaptivecard(workflow, params, summary_params, projectDir, log) { + def hook_url = params.hook_url + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = workflow.manifest.version + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + def hf = new File("$projectDir/assets/adaptivecard.json") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } + } + + // + // Print pipeline summary on completion + // + public static void summary(workflow, params, log) { + Map colors = logColours(params.monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + } + + // + // ANSII Colours used for terminal logging + // + public static Map logColours(Boolean monochrome_logs) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes + } + + // + // Does what is says on the tin + // + public static String dashedLine(monochrome_logs) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" + } + + // + // nf-core logo + // + public static String logo(workflow, monochrome_logs) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) + } +} diff --git a/lib/Utils.groovy b/lib/Utils.groovy new file mode 100644 index 0000000..8d030f4 --- /dev/null +++ b/lib/Utils.groovy @@ -0,0 +1,47 @@ +// +// This file holds several Groovy functions that could be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml + +class Utils { + + // + // When running with -profile conda, warn if channels have not been set-up appropriately + // + public static void checkCondaChannels(log) { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } + } +} diff --git a/lib/WorkflowHlatyping.groovy b/lib/WorkflowHlatyping.groovy new file mode 100755 index 0000000..63152ac --- /dev/null +++ b/lib/WorkflowHlatyping.groovy @@ -0,0 +1,76 @@ +// +// This file holds several functions specific to the workflow/hlatyping.nf in the nf-core/hlatyping pipeline +// + +import groovy.text.SimpleTemplateEngine + +class WorkflowHlatyping { + + // + // Check and validate parameters + // + public static void initialise(params, log) { + genomeExistsError(params, log) + + //if (!params.fasta) { + // log.error "HLA fasta file not specified with e.g. '--fasta hla.fa' or via a detectable config file." + // System.exit(1) + //} + } + + // + // Get workflow summary for MultiQC + // + public static String paramsSummaryMultiqc(workflow, summary) { + String summary_section = '' + for (group in summary.keySet()) { + def group_params = summary.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

$group

\n" + summary_section += "
\n" + for (param in group_params.keySet()) { + summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" + } + summary_section += "
\n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + return yaml_file_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html + }// + // Exit pipeline if incorrect --genome key provided + // + private static void genomeExistsError(params, log) { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + System.exit(1) + } + } +} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy new file mode 100755 index 0000000..cb656e3 --- /dev/null +++ b/lib/WorkflowMain.groovy @@ -0,0 +1,93 @@ +// +// This file holds several functions specific to the main.nf workflow in the nf-core/hlatyping pipeline +// + +class WorkflowMain { + + // + // Citation string for pipeline + // + public static String citation(workflow) { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + '* The pipeline\n' + + ' https://doi.org/10.5281/zenodo.1401039-1073c8\n\n' + + '* The nf-core framework\n' + + ' https://doi.org/10.1038/s41587-020-0439-x\n\n' + + '* Software dependencies\n' + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + } + + // + // Print help to screen if required + // + public static String help(workflow, params, log) { + def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + def help_string = '' + help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) + help_string += NfcoreSchema.paramsHelp(workflow, params, command) + help_string += '\n' + citation(workflow) + '\n' + help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) + return help_string + } + + // + // Print parameter summary log to screen + // + public static String paramsSummaryLog(workflow, params, log) { + def summary_log = '' + summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) + summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) + summary_log += '\n' + citation(workflow) + '\n' + summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) + return summary_log + } + + // + // Validate parameters and print summary to screen + // + public static void initialise(workflow, params, log) { + // Print help to screen if required + if (params.help) { + log.info help(workflow, params, log) + System.exit(0) + } + + // Validate workflow parameters via the JSON schema + if (params.validate_params) { + NfcoreSchema.validateParameters(workflow, params, log) + } + + // Print parameter summary log to screen + + log.info paramsSummaryLog(workflow, params, log) + + // Check that a -profile or Nextflow config has been provided to run the pipeline + NfcoreTemplate.checkConfigProvided(workflow, log) + + // Check that conda channels are set-up correctly + if (params.enable_conda) { + Utils.checkCondaChannels(log) + } + + // Check AWS batch settings + NfcoreTemplate.awsBatch(workflow, params) + + // Check input has been provided + if (!params.input) { + log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" + System.exit(1) + } + } + // + // Get attribute from genome config file e.g. fasta + // + public static Object getGenomeAttribute(params, attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null + } + +} diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar new file mode 100644 index 0000000..805c8bb Binary files /dev/null and b/lib/nfcore_external_java_deps.jar differ diff --git a/main.nf b/main.nf index 284a0fb..f9c7df3 100644 --- a/main.nf +++ b/main.nf @@ -1,585 +1,65 @@ #!/usr/bin/env nextflow /* -======================================================================================== - nf-core/hlatyping -======================================================================================== - nf-core/hlatyping Analysis Pipeline. - #### Homepage / Documentation - https://github.com/nf-core/hlatyping +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + nf-core/hlatyping +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Github : https://github.com/nf-core/hlatyping + + Website: https://nf-co.re/hlatyping + Slack : https://nfcore.slack.com/channels/hlatyping ---------------------------------------------------------------------------------------- */ -def helpMessage() { - log.info nfcoreHeader() - log.info""" - - Usage: - - The typical command for running the pipeline is as follows: - - nextflow run nf-core/hlatyping --input '*_R{1,2}.fastq.gz' -profile docker - - Mandatory arguments: - --input [file] Path to input FastQ or BAM file(s). The path must be enclosed in quotes. - -profile [str] Configuration profile to use. Can use multiple (comma separated). - Options: conda, docker, singularity, test, awsbatch, and more - - Main options: - --single_end [bool] Specifies that the input is single-end reads. - Default: ${params.single_end} - --bam [bool] Specifies that the input is in BAM format. - Default: ${params.bam} - --seqtype [str] Specifies whether the input is DNA or RNA. Options: 'dna', 'rna' - Default: '${params.seqtype}' - --solver [str] Specifies the integer programming solver. Options: 'glpk', 'cbc' - Default: '${params.solver}' - --enumerations [int] Specifies the number of output solutions. - Default: ${params.enumerations} - - Reference genome options: - --base_index_path [str] Path for the mapping reference index location. - --base_index_name [str] Name of the mapping reference index. - - Resource options: - --max_memory [str] Maximum amount of memory that can be requested for any single job (format integer.unit). - Default: '${params.max_memory}' - --max_time [str] Maximum amount of time that can be requested for any single job (format integer.unit). - Default: '${params.max_time}' - --max_cpus [int] Maximum number of CPUs that can be requested for any single job. - Default: ${params.max_cpus} - - Other options: - --outdir [file] The output directory where the results will be saved. - --publish_dir_mode [str] Mode for publishing results in the output directory. Available: symlink, rellink, link, copy, copyNoFollow, move - Default: copy - --email [email] Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. - --email_on_fail [email] Same as --email, except only send mail if the workflow is not successful. - --plaintext_email [bool] Send plain-text email instead of HTML. - --max_multiqc_email_size [str] Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached - Default: 25MB - --monochrome_logs [bool] Do not use coloured log outputs. - --multiqc_config [str] Custom config file to supply to MultiQC. - --tracedir [str] Directory to keep pipeline Nextflow logs and reports. - Default: "${params.outdir}/pipeline_info" - -name [str] Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. - - AWSBatch options: - --awsqueue [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch. - --awsregion [str] The AWS Region for your AWS Batch job to run on. - --awscli [str] Path to the AWS CLI tool. - """.stripIndent() -} - -// Show help message -if (params.help) { - helpMessage() - exit 0 -} - -/* - * SET UP CONFIGURATION VARIABLES - */ -// Validate inputs -params.input ?: params.input_paths ?: { log.error "No read data provided. Make sure you have used the '--input' option."; exit 1 }() -(params.seqtype == 'rna' || params.seqtype == 'dna') ?: { log.error "No or incorrect sequence type provided, you need to add '--seqtype 'dna'' or '--seqtype 'rna''."; exit 1 }() - -// Set mapping index base name according to sequencing type -base_index_name = params.base_index_name ? params.base_index_name : "hla_reference_${params.seqtype}" - -// Has the run name been specified by the user? -// this has the bonus effect of catching both -name and --name -custom_runName = params.name -if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) { - custom_runName = workflow.runName -} - -// Check AWS batch settings -if (workflow.profile.contains('awsbatch')) { - // AWSBatch sanity checking - if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - // related: https://github.com/nextflow-io/nextflow/issues/813 - if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - // Prevent trace files to be stored on S3 since S3 does not support rolling files. - if (params.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles." -} - -// Stage config files -ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() -ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true) -ch_output_docs_images = file("$baseDir/docs/images/", checkIfExists: true) - -/* - * Create a channel for input read files - */ -if( params.input_paths ){ - if( params.single_end || params.bam) { - Channel - .from( params.input_paths ) - .map { row -> [ row[0], [ file( row[1][0], checkIfExists: true ) ] ] } - .ifEmpty { exit 1, "params.input_paths or params.bams was empty - no input files supplied!" } - .set { input_data } - } else { - Channel - .from( params.input_paths ) - .map { row -> [ row[0], [ file( row[1][0], checkIfExists: true), file( row[1][1], checkIfExists: true) ] ] } - .ifEmpty { exit 1, "params.input_paths or params.bams was empty - no input files supplied!" } - .set { input_data } - } -} else if (!params.bam){ - Channel - .fromFilePairs( params.input, size: params.single_end ? 1 : 2 ) - .ifEmpty { exit 1, "Cannot find any reads matching: ${params.input}\nNB: Path needs" + - "to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nIf this is single-end data, please specify --single_end on the command line." } - .set { input_data } -} else { - Channel - .fromPath( params.input ) - .map { row -> [ file(row).baseName, [ file( row, checkIfExists: true ) ] ] } - .ifEmpty { exit 1, "Cannot find any bam file matching: ${params.input}\nNB: Path needs" + - "to be enclosed in quotes!\n" } - .dump() //For debugging purposes - .set { input_data } -} - -if( params.bam ) log.info "BAM file format detected. Initiate remapping to HLA alleles with yara mapper." - -// Header log info -log.info nfcoreHeader() -def summary = [:] -if (workflow.revision) summary['Pipeline Release'] = workflow.revision -summary['Run Name'] = custom_runName ?: workflow.runName -summary['File Type'] = params.bam ? 'BAM' : 'Other (fastq, fastq.gz, ...)' -summary['Seq Type'] = params.seqtype -summary['Index Location'] = "$params.base_index_path/$base_index_name" -summary['IP Solver'] = params.solver -summary['Enumerations'] = params.enumerations -summary['Beta'] = params.beta -summary['Max Memory'] = params.max_memory -summary['Max CPUs'] = params.max_cpus -summary['Max Time'] = params.max_time -summary['Input'] = params.input_paths ? params.input_paths : params.input -summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End' -summary['Output Dir'] = params.outdir -summary['Launch Dir'] = workflow.launchDir -summary['Working Dir'] = workflow.workDir -summary['Script Dir'] = workflow.projectDir -summary['User'] = workflow.userName -summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job" -if(workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container" -if (workflow.profile.contains('awsbatch')) { - summary['AWS Region'] = params.awsregion - summary['AWS Queue'] = params.awsqueue - summary['AWS CLI'] = params.awscli -} -summary['Config Profile'] = workflow.profile -if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description -if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact -if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url -summary['Config Files'] = workflow.configFiles.join(', ') -if (params.email || params.email_on_fail) { - summary['E-mail Address'] = params.email - summary['E-mail on Failure'] = params.email_on_fail - summary['MultiQC Maxsize'] = params.max_multiqc_email_size -} -log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n") -log.info "-\033[2m--------------------------------------------------\033[0m-" - -// Check the hostnames against configured profiles -checkHostname() - -Channel.from(summary.collect{ [it.key, it.value] }) - .map { k,v -> "
    $k
    ${v ?: 'N/A'}
    " } - .reduce { a, b -> return [a, b].join("\n ") } - .map { x -> """ - id: 'nf-core-hlatyping-summary' - description: " - this information is collected when the pipeline is started." - section_name: 'nf-core/hlatyping Workflow Summary' - section_href: 'https://github.com/nf-core/hlatyping' - plot_type: 'html' - data: | -
    - $x -
    - """.stripIndent() } - .set { ch_workflow_summary } - -if( params.bam ) log.info "BAM file format detected. Initiate remapping to HLA alleles with yara mapper." - -/* - * Preparation - Unpack files if packed. - * - * OptiType cannot handle *.gz archives as input files, - * So we have to unpack first, if this is the case. - */ -if ( !params.bam ) { // FASTQ files processing - process unzip { - - input: - set val(pattern), file(reads) from input_data - - output: - set val(pattern), "unzipped_{1,2}.fastq" into raw_reads - - script: - if(params.single_end) - """ - zcat ${reads[0]} > unzipped_1.fastq - """ - else - """ - zcat ${reads[0]} > unzipped_1.fastq - zcat ${reads[1]} > unzipped_2.fastq - """ - } -} else { // BAM files processing - - /* - * Preparation - Remapping of reads against HLA reference and filtering these - * - * In case the user provides BAM files, a remapping step - * is then done against the HLA reference sequence. - */ - process remap_to_hla { - label 'process_medium' - - input: - path(data_index) from params.base_index_path - set val(pattern), file(bams) from input_data - output: - set val(pattern), "mapped_{1,2}.bam" into fished_reads - - script: - def full_index = "$data_index/$base_index_name" - if (params.single_end) - """ - samtools bam2fq $bams > output_1.fastq - yara_mapper -e 3 -t ${task.cpus} -f bam $full_index output_1.fastq > output_1.bam - samtools view -@ ${task.cpus} -h -F 4 -b1 output_1.bam > mapped_1.bam - """ - else - """ - samtools view -@ ${task.cpus} -h -f 0x40 $bams > output_1.bam - samtools view -@ ${task.cpus} -h -f 0x80 $bams > output_2.bam - samtools bam2fq output_1.bam > output_1.fastq - samtools bam2fq output_2.bam > output_2.fastq - yara_mapper -e 3 -t ${task.cpus} -f bam $full_index output_1.fastq output_2.fastq > output.bam - samtools view -@ ${task.cpus} -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam - samtools view -@ ${task.cpus} -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam - """ - } -} - - -/* - * STEP 1 - Create config.ini for Optitype - * - * Optitype requires a config.ini file with information like - * which solver to use for the optimization step. Also, the number - * of threads is specified there for different steps. - * As we do not want to touch the original source code of Optitype, - * we simply take information from Nextflow about the available resources - * and create a small config.ini as first stepm which is then passed to Optitype. - */ -process make_ot_config { - publishDir "${params.outdir}/config", mode: params.publish_dir_mode - - output: - file 'config.ini' into config - - script: - """ - configbuilder --max-cpus ${params.max_cpus} --solver ${params.solver} > config.ini - """ -} +nextflow.enable.dsl = 2 /* - * Preparation Step - Pre-mapping against HLA - * - * In order to avoid the internal usage of RazerS from within OptiType when - * the input files are of type `fastq`, we perform a pre-mapping step - * here with the `yara` mapper, and map against the HLA reference only. - * - */ -if (!params.bam) - process pre_map_hla { - label 'process_medium' - - input: - path(data_index) from params.base_index_path - set val(pattern), file(reads) from raw_reads - - output: - set val(pattern), "mapped_{1,2}.bam" into fished_reads +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + GENOME PARAMETER VALUES +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ - script: - def full_index = "$data_index/$base_index_name" - if (params.single_end) - """ - yara_mapper -e 3 -t ${task.cpus} -f bam $full_index $reads > output_1.bam - samtools view -@ ${task.cpus} -h -F 4 -b1 output_1.bam > mapped_1.bam - """ - else - """ - yara_mapper -e 3 -t ${task.cpus} -f bam $full_index $reads > output.bam - samtools view -@ ${task.cpus} -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam - samtools view -@ ${task.cpus} -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam - """ - } +// might be needed again +//params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') /* - * STEP 2 - Run Optitype - * - * This is the major process, that formulates the IP and calls the selected - * IP solver. - * - * Ouput formats: - */ -process run_optitype { - publishDir "${params.outdir}/optitype/", mode: params.publish_dir_mode - - input: - file 'config.ini' from config - set val(pattern), file(reads) from fished_reads - - output: - file "${pattern}" +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + VALIDATE & PRINT PARAMETER SUMMARY +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ - script: - """ - OptiTypePipeline.py -i ${reads} -e ${params.enumerations} -b ${params.beta} \\ - -p "${pattern}" -c config.ini --${params.seqtype} --outdir ${pattern} - """ -} +WorkflowMain.initialise(workflow, params, log) /* - * - * Output Description HTML - */ -process output_documentation { - publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode - - input: - file output_docs from ch_output_docs - file images from ch_output_docs_images +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + NAMED WORKFLOW FOR PIPELINE +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ - output: - file "results_description.html" +include { HLATYPING } from './workflows/hlatyping' - script: - """ - markdown_to_html.py $output_docs -o results_description.html - """ +// +// WORKFLOW: Run main nf-core/hlatyping analysis pipeline +// +workflow NFCORE_HLATYPING { + HLATYPING () } /* - * Parse software version numbers - */ -process get_software_versions { - publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode, - saveAs: { filename -> - if (filename.indexOf(".csv") > 0) filename - else null - } - - output: - file 'software_versions_mqc.yaml' into ch_software_versions_yaml - file "software_versions.csv" - - script: - """ - echo $workflow.manifest.version > v_pipeline.txt - echo $workflow.nextflow.version > v_nextflow.txt - multiqc --version &> v_multiqc.txt 2>&1 || true - samtools --version &> v_samtools.txt 2>&1 || true - yara_mapper --help &> v_yara.txt 2>&1 || true - cat \$(which OptiTypePipeline.py) &> v_optitype.txt 2>&1 || true - scrape_software_versions.py &> software_versions_mqc.yaml - """ -} - -process multiqc { - publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode - - input: - file (multiqc_config) from ch_multiqc_config - file mqc_custom_config from ch_multiqc_custom_config.collect().ifEmpty([]) - file ('software_versions/*') from ch_software_versions_yaml.collect() - file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml") - - output: - file "*multiqc_report.html" into ch_multiqc_report - file "*_data" - file "multiqc_plots" +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ - script: - rtitle = custom_runName ? "--title \"$custom_runName\"" : '' - rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : '' - custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : '' - """ - multiqc -f $rtitle $rfilename $custom_config_file . - """ +// +// WORKFLOW: Execute a single named workflow for the pipeline +// See: https://github.com/nf-core/rnaseq/issues/619 +// +workflow { + NFCORE_HLATYPING () } /* -* Completion e-mail notification +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -workflow.onComplete { - - // Set up the e-mail variables - def subject = "[nf-core/hlatyping] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[nf-core/hlatyping] FAILED: $workflow.runName" - } - def email_fields = [:] - email_fields['version'] = workflow.manifest.version - email_fields['runName'] = custom_runName ?: workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary - email_fields['summary']['Date Started'] = workflow.start - email_fields['summary']['Date Completed'] = workflow.complete - email_fields['summary']['Pipeline script file path'] = workflow.scriptFile - email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision - email_fields['summary']['Nextflow Version'] = workflow.nextflow.version - email_fields['summary']['Nextflow Build'] = workflow.nextflow.build - email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = ch_multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList) { - log.warn "[nf-core/hlatyping] Found multiple reports from process 'multiqc', will use only one" - mqc_report = mqc_report[0] - } - } - } catch (all) { - log.warn "[nf-core/hlatyping] Could not attach MultiQC report to summary email" - } - - // Check if we are only sending emails on failure - email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$baseDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$baseDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ] - def sf = new File("$baseDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "[nf-core/hlatyping] Sent summary e-mail to $email_address (sendmail)" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "[nf-core/hlatyping] Sent summary e-mail to $email_address (mail)" - } - } - - // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - - c_green = params.monochrome_logs ? '' : "\033[0;32m"; - c_purple = params.monochrome_logs ? '' : "\033[0;35m"; - c_red = params.monochrome_logs ? '' : "\033[0;31m"; - c_reset = params.monochrome_logs ? '' : "\033[0m"; - - if (workflow.stats.ignoredCount > 0 && workflow.success) { - log.info "-${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}-" - log.info "-${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}-" - log.info "-${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}-" - } - - if (workflow.success) { - log.info "-${c_purple}[nf-core/hlatyping]${c_green} Pipeline completed successfully${c_reset}-" - } else { - checkHostname() - log.info "-${c_purple}[nf-core/hlatyping]${c_red} Pipeline completed with errors${c_reset}-" - } -} - - -def nfcoreHeader() { - // Log colors ANSI codes - c_black = params.monochrome_logs ? '' : "\033[0;30m"; - c_blue = params.monochrome_logs ? '' : "\033[0;34m"; - c_cyan = params.monochrome_logs ? '' : "\033[0;36m"; - c_dim = params.monochrome_logs ? '' : "\033[2m"; - c_green = params.monochrome_logs ? '' : "\033[0;32m"; - c_purple = params.monochrome_logs ? '' : "\033[0;35m"; - c_reset = params.monochrome_logs ? '' : "\033[0m"; - c_white = params.monochrome_logs ? '' : "\033[0;37m"; - c_yellow = params.monochrome_logs ? '' : "\033[0;33m"; - - return """ -${c_dim}--------------------------------------------------${c_reset}- - ${c_green},--.${c_black}/${c_green},-.${c_reset} - ${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset} - ${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset} - ${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset} - ${c_green}`._,._,\'${c_reset} - ${c_purple} nf-core/hlatyping v${workflow.manifest.version}${c_reset} - -${c_dim}--------------------------------------------------${c_reset}- - """.stripIndent() -} - -def checkHostname() { - def c_reset = params.monochrome_logs ? '' : "\033[0m" - def c_white = params.monochrome_logs ? '' : "\033[0;37m" - def c_red = params.monochrome_logs ? '' : "\033[1;91m" - def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m" - if (params.hostnames) { - def hostname = "hostname".execute().text.trim() - params.hostnames.each { prof, hnames -> - hnames.each { hname -> - if (hostname.contains(hname) && !workflow.profile.contains(prof)) { - log.error "====================================================\n" + - " ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" + - " but your machine hostname is ${c_white}'$hostname'${c_reset}\n" + - " ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" + - "============================================================" - } - } - } - } -} diff --git a/modules.json b/modules.json new file mode 100644 index 0000000..1190071 --- /dev/null +++ b/modules.json @@ -0,0 +1,48 @@ +{ + "name": "nf-core/hlatyping", + "homePage": "https://github.com/nf-core/hlatyping", + "repos": { + "https://github.com/nf-core/modules.git": { + "modules": { + "nf-core": { + "custom/dumpsoftwareversions": { + "branch": "master", + "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0" + }, + "fastqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "gunzip": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "multiqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "optitype": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "samtools/collatefastq": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "samtools/view": { + "branch": "master", + "git_sha": "202683bfc98ddecdd456ea73268e330bca2e5c5a" + }, + "yara/index": { + "branch": "master", + "git_sha": "6a5ea5708e1d7891bb71026eba98508866339d1e" + }, + "yara/mapper": { + "branch": "master", + "git_sha": "6a5ea5708e1d7891bb71026eba98508866339d1e" + } + } + } + } + } +} diff --git a/modules/local/check_paired.nf b/modules/local/check_paired.nf new file mode 100644 index 0000000..a002af9 --- /dev/null +++ b/modules/local/check_paired.nf @@ -0,0 +1,30 @@ +process CHECK_PAIRED { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_0' : + 'quay.io/biocontainers/samtools:1.16.1--h6899075_0' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path(input), path("is_singleend.txt"), emit:reads + path "versions.yml", emit: versions + + script: + """ + if [ \$({ samtools view -H $input -@$task.cpus ; samtools view $input -@$task.cpus | head -n1000; } | samtools view -c -f 1 -@$task.cpus ) -gt 0 ]; then + echo false > is_singleend.txt + else + echo true > is_singleend.txt + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf new file mode 100644 index 0000000..4daa800 --- /dev/null +++ b/modules/local/samplesheet_check.nf @@ -0,0 +1,27 @@ +process SAMPLESHEET_CHECK { + tag "$samplesheet" + + conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'quay.io/biocontainers/python:3.8.3' }" + + input: + path samplesheet + + output: + path '*.csv' , emit: csv + path "versions.yml", emit: versions + + script: // This script is bundled with the pipeline, in nf-core/hlatyping/bin/ + """ + check_samplesheet.py \\ + $samplesheet \\ + samplesheet.valid.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf new file mode 100644 index 0000000..cebb6e0 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -0,0 +1,24 @@ +process CUSTOM_DUMPSOFTWAREVERSIONS { + label 'process_single' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + + input: + path versions + + output: + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + template 'dumpsoftwareversions.py' +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml new file mode 100644 index 0000000..60b546a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -0,0 +1,34 @@ +name: custom_dumpsoftwareversions +description: Custom module used to dump software versions within the nf-core pipeline template +keywords: + - custom + - version +tools: + - custom: + description: Custom module used to dump software versions within the nf-core pipeline template + homepage: https://github.com/nf-core/tools + documentation: https://github.com/nf-core/tools + licence: ["MIT"] +input: + - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" + +output: + - yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" + - mqc_yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py new file mode 100755 index 0000000..da03340 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python + + +"""Provide functions to merge multiple versions.yml files.""" + + +import yaml +import platform +from textwrap import dedent + + +def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" + html = [ + dedent( + """\\ + + + + + + + + + + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + + + + + + """ + ) + ) + html.append("") + html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") + return "\\n".join(html) + + +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf new file mode 100644 index 0000000..0573036 --- /dev/null +++ b/modules/nf-core/fastqc/main.nf @@ -0,0 +1,59 @@ +process FASTQC { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + 'quay.io/biocontainers/fastqc:0.11.9--0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + // Add soft-links to original FastQs for consistent naming in pipeline + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + """ + [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + fastqc $args --threads $task.cpus ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + } else { + """ + [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz + [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz + fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml new file mode 100644 index 0000000..4da5bb5 --- /dev/null +++ b/modules/nf-core/fastqc/meta.yml @@ -0,0 +1,52 @@ +name: fastqc +description: Run FastQC on sequenced reads +keywords: + - quality control + - qc + - adapters + - fastq +tools: + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf new file mode 100644 index 0000000..fa6ba26 --- /dev/null +++ b/modules/nf-core/gunzip/main.nf @@ -0,0 +1,44 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + gunzip = archive.toString() - '.gz' + """ + gunzip \\ + -f \\ + $args \\ + $archive + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + gunzip = archive.toString() - '.gz' + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml new file mode 100644 index 0000000..4d2ebc8 --- /dev/null +++ b/modules/nf-core/gunzip/meta.yml @@ -0,0 +1,34 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf new file mode 100644 index 0000000..a8159a5 --- /dev/null +++ b/modules/nf-core/multiqc/main.nf @@ -0,0 +1,53 @@ +process MULTIQC { + label 'process_single' + + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + + input: + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + + output: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + """ + multiqc \\ + --force \\ + $args \\ + $config \\ + $extra_config \\ + . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml new file mode 100644 index 0000000..ebc29b2 --- /dev/null +++ b/modules/nf-core/multiqc/meta.yml @@ -0,0 +1,55 @@ +name: MultiQC +description: Aggregate results from bioinformatics analyses across many samples into a single report +keywords: + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report +tools: + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] + +input: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + +output: + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf new file mode 100644 index 0000000..b6a3e20 --- /dev/null +++ b/modules/nf-core/optitype/main.nf @@ -0,0 +1,49 @@ +process OPTITYPE { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : + 'quay.io/biocontainers/optitype:1.3.5--0' }" + + input: + tuple val(meta), path(bam), path(bai) + + output: + tuple val(meta), path("${prefix}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + """ + # Create a config for OptiType on a per sample basis with task.ext.args2 + + #Doing it old school now + echo "[mapping]" > config.ini + echo "razers3=razers3" >> config.ini + echo "threads=$task.cpus" >> config.ini + echo "[ilp]" >> config.ini + echo "$args2" >> config.ini + echo "threads=1" >> config.ini + echo "[behavior]" >> config.ini + echo "deletebam=true" >> config.ini + echo "unpaired_weight=0" >> config.ini + echo "use_discordant=false" >> config.ini + + # Run the actual OptiType typing with args + OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $args --prefix $prefix --outdir $prefix + + #Couldn't find a nicer way of doing this + cat <<-END_VERSIONS > versions.yml + "${task.process}": + optitype: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/optitype/meta.yml b/modules/nf-core/optitype/meta.yml new file mode 100644 index 0000000..9ca1077 --- /dev/null +++ b/modules/nf-core/optitype/meta.yml @@ -0,0 +1,50 @@ +name: optitype +description: Perform HLA-I typing of sequencing data +keywords: + - hla-typing + - ILP + - HLA-I +tools: + - optitype: + description: Precision HLA typing from next-generation sequencing data + homepage: https://github.com/FRED-2/OptiType + documentation: https://github.com/FRED-2/OptiType + doi: "10.1093/bioinformatics/btu548" + licence: ["BSD-3-Clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', seq_type:'DNA' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - output: + type: file + description: OptiType Results Folder + pattern: "${prefix}" + - pdf: + type: file + description: OptiType PDF Plots + pattern: "*.pdf" + +authors: + - "@apeltzer" diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf new file mode 100644 index 0000000..3d9becd --- /dev/null +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -0,0 +1,47 @@ +process SAMTOOLS_COLLATEFASTQ { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + + input: + tuple val(meta), path(input) + + output: + //TODO might be good to have ordered output of the fastq files, so we can + // make sure the we get the right files + tuple val(meta), path("*_{1,2}.fq.gz"), path("*_other.fq.gz"), path("*_singleton.fq.gz"), emit: reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + samtools collate \\ + $args \\ + --threads $task.cpus \\ + -O \\ + $input \\ + . | + + samtools fastq \\ + $args2 \\ + --threads $task.cpus \\ + -1 ${prefix}_1.fq.gz \\ + -2 ${prefix}_2.fq.gz \\ + -0 ${prefix}_other.fq.gz \\ + -s ${prefix}_singleton.fq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/collatefastq/meta.yml b/modules/nf-core/samtools/collatefastq/meta.yml new file mode 100644 index 0000000..d3a2e3a --- /dev/null +++ b/modules/nf-core/samtools/collatefastq/meta.yml @@ -0,0 +1,48 @@ +name: samtools_collatefastq +description: | + The module uses collate and then fastq methods from samtools to + convert a SAM, BAM or CRAM file to FASTQ format +keywords: + - bam2fq + - samtools + - fastq +tools: + - samtools: + description: Tools for dealing with SAM, BAM and CRAM files + homepage: None + documentation: http://www.htslib.org/doc/1.1/samtools.html + tool_dev_url: None + doi: "" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) + or a single interleaved .fq.gz file if the user chooses not to split the reads. + pattern: "*.fq.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@lescai" + - "@maxulysse" diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf new file mode 100644 index 0000000..b2f5c67 --- /dev/null +++ b/modules/nf-core/samtools/view/main.nf @@ -0,0 +1,66 @@ +process SAMTOOLS_VIEW { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + + input: + tuple val(meta), path(input), path(index) + path fasta + path qname + + output: + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.sam"), emit: sam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--reference ${fasta}" : "" + def readnames = qname ? "--qname-file ${qname}": "" + def file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools \\ + view \\ + --threads ${task.cpus-1} \\ + ${reference} \\ + ${readnames} \\ + $args \\ + -o ${prefix}.${file_type} \\ + $input \\ + $args2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + touch ${prefix}.cram + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml new file mode 100644 index 0000000..a52e4f8 --- /dev/null +++ b/modules/nf-core/samtools/view/meta.yml @@ -0,0 +1,79 @@ +name: samtools_view +description: filter/convert SAM/BAM/CRAM file +keywords: + - view + - bam + - sam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: optional file + description: BAM.BAI/CRAM.CRAI file + pattern: "*.{.bai,.crai}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" + - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: optional filtered/converted BAM file + pattern: "*.{bam}" + - cram: + type: file + description: optional filtered/converted CRAM file + pattern: "*.{cram}" + - sam: + type: file + description: optional filtered/converted SAM file + pattern: "*.{sam}" + # bai, csi, and crai are created with `--write-index` + - bai: + type: file + description: optional BAM file index + pattern: "*.{bai}" + - csi: + type: file + description: optional tabix BAM file index + pattern: "*.{csi}" + - crai: + type: file + description: optional CRAM file index + pattern: "*.{crai}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" + - "@priyanka-surana" diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf new file mode 100644 index 0000000..b6bae9a --- /dev/null +++ b/modules/nf-core/yara/index/main.nf @@ -0,0 +1,33 @@ +process YARA_INDEX { + tag "$fasta" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : + 'quay.io/biocontainers/yara:1.0.2--2' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("${fasta}*") , emit: index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + + """ + yara_indexer \\ + $fasta \\ + -o ${fasta} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + yara: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/yara/index/meta.yml b/modules/nf-core/yara/index/meta.yml new file mode 100644 index 0000000..bfc74f0 --- /dev/null +++ b/modules/nf-core/yara/index/meta.yml @@ -0,0 +1,34 @@ +name: yara_index +description: Builds a YARA index for a reference genome +keywords: + - build + - index + - fasta + - genome + - reference +tools: + - yara: + description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + homepage: https://github.com/seqan/seqan + documentation: https://github.com/seqan/seqan + tool_dev_url: https://github.com/seqan/seqan + doi: "" + licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + +input: + - fasta: + type: file + description: Input genome fasta file + +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - index: + type: file + description: YARA genome index files + pattern: "yara.*" + +authors: + - "@apeltzer" diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf new file mode 100644 index 0000000..c2624ab --- /dev/null +++ b/modules/nf-core/yara/mapper/main.nf @@ -0,0 +1,66 @@ +process YARA_MAPPER { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : + 'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(index) + + output: + tuple val(meta), path("*.mapped.bam"), emit: bam + tuple val(meta), path("*.mapped.bam.bai"), emit: bai + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def index_prefix = index[0].baseName.substring(0,index[0].baseName.lastIndexOf('.')) + if (meta.single_end) { + """ + yara_mapper \\ + $args \\ + -t $task.cpus \\ + -f bam \\ + ${index_prefix} \\ + $reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam + + samtools index -@ $task.cpus ${prefix}.mapped.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + } else { + """ + yara_mapper \\ + $args \\ + -t $task.cpus \\ + -f bam \\ + ${index_prefix} \\ + ${reads[0]} \\ + ${reads[1]} > output.bam + + samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam + samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam + + samtools index -@ $task.cpus ${prefix}_1.mapped.bam + samtools index -@ $task.cpus ${prefix}_2.mapped.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + } +} diff --git a/modules/nf-core/yara/mapper/meta.yml b/modules/nf-core/yara/mapper/meta.yml new file mode 100644 index 0000000..0c4c0d4 --- /dev/null +++ b/modules/nf-core/yara/mapper/meta.yml @@ -0,0 +1,51 @@ +name: yara_mapper +description: Align reads to a reference genome using YARA +keywords: + - align + - genome + - reference +tools: + - yara: + description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + homepage: https://github.com/seqan/seqan + documentation: https://github.com/seqan/seqan + tool_dev_url: https://github.com/seqan/seqan + doi: "" + licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: YARA genome index files + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Sorted BAM file index + pattern: "*.{bai}" + +authors: + - "@apeltzer" diff --git a/nextflow.config b/nextflow.config index fc610d0..3c6a28b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,158 +1,238 @@ /* - * ------------------------------------------------- - * nf-core/hlatyping Nextflow config file - * ------------------------------------------------- - * Default config options for all environments. - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + nf-core/hlatyping Nextflow config file +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Default config options for all compute environments +---------------------------------------------------------------------------------------- +*/ // Global default params, used in configs params { - // Workflow flags - input = '' - single_end = false - outdir = './results' - publish_dir_mode = 'copy' - bam = false - input_paths = '' - seqtype = 'dna' - solver = 'glpk' - enumerations = 1 - beta = 0.009 - //use this to combine accordingly for dna/rna samples - base_index_path = "$baseDir/data/indices/yara" - base_index_name = '' - - // Boilerplate options - name = false - multiqc_config = false - email = false - email_on_fail = false - max_multiqc_email_size = 25.MB - plaintext_email = false - monochrome_logs = false - help = false - tracedir = "${params.outdir}/pipeline_info" - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = true - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - hostnames = false - config_profile_description = false - config_profile_contact = false - config_profile_url = false - - // Defaults only, expecting to be overwritten - max_memory = 128.GB - max_cpus = 16 - max_time = 240.h -} -// Container slug. Stable releases should specify release tag! -// Developmental code should specify :dev -process.container = 'nfcore/hlatyping:1.2.0' + // Input options + input = null + + // Optimisation steps + solver = 'glpk' + enumerations = 1 + beta = 0.009 + + // References + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_ignore = false + + // MultiQC options + multiqc_config = "$projectDir/assets/multiqc_optitype_config.yml" + multiqc_title = null + multiqc_logo = "${projectDir}/assets/nf-core-hlatyping_logo_light.png" + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null + + // Boilerplate options + outdir = null + tracedir = "${params.outdir}/pipeline_info" + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + validate_params = true + show_hidden_params = false + schema_ignore_params = 'genomes' + enable_conda = false + + + // Config options + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_description = null + config_profile_contact = null + config_profile_url = null + config_profile_name = null + + + // Max resource options + // Defaults only, expecting to be overwritten + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' + +} // Load base.config by default for all pipelines includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" + includeConfig "${params.custom_config_base}/nfcore_custom.config" } catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") + System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } +// Load nf-core/hlatyping custom profiles from different institutions. +// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// try { +// includeConfig "${params.custom_config_base}/pipeline/hlatyping.config" +// } catch (Exception e) { +// System.err.println("WARNING: Could not load nf-core/config/hlatyping profiles: ${params.custom_config_base}/pipeline/hlatyping.config") +// } + + profiles { - conda { process.conda = "$baseDir/environment.yml" } - debug { process.beforeScript = 'echo $HOSTNAME' } - docker { - docker.enabled = true - // Avoid this error: - // WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. - // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351 - // once this is established and works well, nextflow might implement this behavior as new default. - docker.runOptions = '-u \$(id -u):\$(id -g)' - } - singularity { - singularity.enabled = true - singularity.autoMounts = true - } - test { includeConfig 'conf/test.config' } - test_fastq { includeConfig 'conf/test_fastq.config'} - test_rna { includeConfig 'conf/test_rna.config'} - test_full { includeConfig 'conf/test_full.config'} + debug { process.beforeScript = 'echo $HOSTNAME' } + conda { + params.enable_conda = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + mamba { + params.enable_conda = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + docker { + docker.enabled = true + docker.userEmulation = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + podman { + podman.enabled = true + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + shifter { + shifter.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + } + charliecloud { + charliecloud.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + } + gitpod { + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB + } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + test_fastq { includeConfig 'conf/test_fastq.config'} + test_rna { includeConfig 'conf/test_rna.config'} + test_dna_rna { includeConfig 'conf/test_dna_rna.config'} } + // Load igenomes.config if required if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' + includeConfig 'conf/igenomes.config' +} else { + params.genomes = [:] } + // Export these variables to prevent local Python/R libraries from conflicting with those in the container +// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. +// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. + env { - PYTHONNOUSERSITE = 1 - R_PROFILE_USER = "/.Rprofile" - R_ENVIRON_USER = "/.Renviron" + PYTHONNOUSERSITE = 1 + R_PROFILE_USER = "/.Rprofile" + R_ENVIRON_USER = "/.Renviron" + JULIA_DEPOT_PATH = "/usr/local/share/julia" } // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { - enabled = true - file = "${params.tracedir}/execution_timeline.html" + enabled = true + file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" } report { - enabled = true - file = "${params.tracedir}/execution_report.html" + enabled = true + file = "${params.tracedir}/execution_report_${trace_timestamp}.html" } trace { - enabled = true - file = "${params.tracedir}/execution_trace.txt" + enabled = true + file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" } dag { - enabled = true - file = "${params.tracedir}/pipeline_dag.svg" + enabled = true + file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" } manifest { - name = 'nf-core/hlatyping' - author = 'Christopher Mohr, Alexander Peltzer, Sven Fillinger' - homePage = 'https://github.com/nf-core/hlatyping' - description = 'Precision HLA typing from next-generation sequencing data.' - mainScript = 'main.nf' - nextflowVersion = '>=19.10.0' - version = '1.2.0' + name = 'nf-core/hlatyping' + author = 'Christopher Mohr, Alexander Peltzer, Sven Fillinger' + homePage = 'https://github.com/nf-core/hlatyping' + description = 'Precision HLA typing from next-generation sequencing data.' + mainScript = 'main.nf' + nextflowVersion = '!>=21.10.3' + version = '2.0.0' + doi = '' } +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } } - } } diff --git a/nextflow_schema.json b/nextflow_schema.json index 7604a88..af7f283 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "https://json-schema.org/draft-07/schema", + "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/hlatyping/master/nextflow_schema.json", "title": "nf-core/hlatyping pipeline parameters", "description": "Precision HLA typing from next-generation sequencing data.", @@ -10,46 +10,22 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", - "fa_icon": "fas fa-dna", - "description": "Input FastQ or BAM files.", - "help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq'\n```\n\nPlease note the following requirements:\n\n1. The path must be enclosed in quotes\n2. The path must have at least one `*` wildcard character\n3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.\n\nIf left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`" - }, - "input_paths": { - "type": "string", - "fa_icon": "fas fa-dna", - "description": "Input multiple FastQ or BAM files.", - "default": "undefined", - "hidden": true - }, - "single_end": { - "type": "boolean", - "description": "Specifies that the input is single-end reads.", - "fa_icon": "fas fa-align-center", - "help_text": "By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--input`. For example:\n\n```bash\n--single_end --input '*.fastq'\n```\n\nIt is not possible to run a mixture of single-end and paired-end files in one run." - }, - "bam": { - "type": "boolean", - "description": "Specifies that the input is in BAM format.", - "help_text": "By default, the pipeline expects input data as `.fastq{.gz}`. You can also provide `.bam` files as input and combine it with the `--single_end` option, if necessary.\n\nThis will trigger the pipeline to extract the reads from the `.bam` file and remap them against the HLA reference sequence, using the `yara` mapper. Indices and references are shipped with this pipeline.", - "fa_icon": "fas fa-file-archive" - }, - "seqtype": { - "type": "string", - "default": "dna", - "description": "Specifies whether the input is DNA or RNA.", - "help_text": "By default, the pipeline assumes `DNA` as input sequence type. In case you want to use `RNA` data as input, just provide the option with `--seqtype 'rna'`.", - "fa_icon": "fas fa-vials" + "format": "file-path", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "schema": "assets/schema_input.json", + "description": "Path to comma-separated file containing information about the samples in the experiment.", + "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hlatyping/usage#samplesheet-input).", + "fa_icon": "fas fa-file-csv" }, "outdir": { "type": "string", - "description": "The output directory where the results will be saved.", - "default": "./results", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, "email": { @@ -61,8 +37,8 @@ } } }, - "optimisation_step_options": { - "title": "Optimisation step options", + "optitype_optimisation_steps": { + "title": "OptiType Optimisation steps", "type": "object", "description": "Options for the optimisation step of the HLA typing pipeline.", "default": "", @@ -77,7 +53,7 @@ }, "enumerations": { "type": "integer", - "default": "1", + "default": 1, "fa_icon": "fas fa-sort-amount-up", "help_text": "By default, the pipeline will do one enumeration (`--enumerations 1`). If you want OptiType to output the optimal solution and the top `N-1` suboptimal solutions in the result file, please specify the number of enumerations accordingly.", "description": "Specifies the number of output solutions." @@ -88,6 +64,11 @@ "fa_icon": "fas fa-braille", "help_text": "By default, the pipeline uses a beta value of `0.009`. The constant beta weights the regularisation term of the underlying integer linear program to account for homozygosity since the formulation favors heterozygous allele combinations. Beta represents the proportion of reads that need to be additionally explained by a chosen allele combination in order to choose heterzygous solutions over homzygous solutions. Evaluation of different values for beta showed the best performance with `0.009`. Please refer to the original publication of OptiType (doi: 10.1093/bioinformatics/btu548) for details.", "description": "Specifies the weight of the regularisation term." + }, + "multiqc_title": { + "type": "string", + "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", + "fa_icon": "fas fa-file-signature" } } }, @@ -95,12 +76,19 @@ "title": "Reference genome options", "type": "object", "fa_icon": "fas fa-dna", - "description": "Options for the reference genome indices used to align reads.", + "description": "Reference genome related files and options required for the workflow.", "properties": { + "genome": { + "type": "string", + "description": "Name of iGenomes reference.", + "fa_icon": "fas fa-book", + "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." + }, "igenomes_base": { "type": "string", + "format": "directory-path", "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes/", + "default": "s3://ngi-igenomes/igenomes", "fa_icon": "fas fa-cloud-download-alt", "hidden": true }, @@ -110,99 +98,54 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." - }, - "base_index_path": { - "type": "string", - "default": "$baseDir/data/indices/yara", - "description": "Path for the mapping reference index location.", - "fa_icon": "far fa-folder" - }, - "base_index_name": { - "type": "string", - "default": "", - "description": "Name of the mapping reference index.", - "fa_icon": "fas fa-file-signature" } } }, - "generic_options": { - "title": "Generic options", + "institutional_config_options": { + "title": "Institutional config options", "type": "object", - "fa_icon": "fas fa-file-import", - "description": "Less common options for the pipeline, typically set in a config file.", - "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralised config profiles. These should not be edited.", + "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "hidden": true, - "fa_icon": "fas fa-question-circle" - }, - "publish_dir_mode": { + "custom_config_version": { "type": "string", - "default": "copy", + "description": "Git commit id for Institutional configs.", + "default": "master", "hidden": true, - "description": "Method used to save pipeline results to output directory.", - "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", - "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ] + "fa_icon": "fas fa-users-cog" }, - "name": { + "custom_config_base": { "type": "string", - "description": "Workflow name.", - "fa_icon": "fas fa-fingerprint", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", "hidden": true, - "help_text": "A custom name for the pipeline run. Unlike the core nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles." + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" }, - "email_on_fail": { + "config_profile_name": { "type": "string", - "description": "Email address for completion summary, only when pipeline fails.", - "fa_icon": "fas fa-exclamation-triangle", - "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", - "hidden": true, - "help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful." - }, - "plaintext_email": { - "type": "boolean", - "description": "Send plain-text email instead of HTML.", - "fa_icon": "fas fa-remove-format", + "description": "Institutional config name.", "hidden": true, - "help_text": "Set to receive plain-text e-mails instead of HTML formatted." + "fa_icon": "fas fa-users-cog" }, - "max_multiqc_email_size": { + "config_profile_description": { "type": "string", - "description": "File size limit when attaching MultiQC reports to summary emails.", - "default": "25.MB", - "fa_icon": "fas fa-file-upload", - "hidden": true, - "help_text": "If file generated by pipeline exceeds the threshold, it will not be attached." - }, - "monochrome_logs": { - "type": "boolean", - "description": "Do not use coloured log outputs.", - "fa_icon": "fas fa-palette", + "description": "Institutional config description.", "hidden": true, - "help_text": "Set to disable colourful command line output and live life in monochrome." + "fa_icon": "fas fa-users-cog" }, - "multiqc_config": { + "config_profile_contact": { "type": "string", - "description": "Custom config file to supply to MultiQC.", - "fa_icon": "fas fa-cog", - "hidden": true + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" }, - "tracedir": { + "config_profile_url": { "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" } } }, @@ -226,6 +169,7 @@ "description": "Maximum amount of memory that can be requested for any single job.", "default": "128.GB", "fa_icon": "fas fa-memory", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", "hidden": true, "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" }, @@ -234,57 +178,112 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", + "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } } }, - "institutional_config_options": { - "title": "Institutional config options", + "generic_options": { + "title": "Generic options", "type": "object", - "fa_icon": "fas fa-university", - "description": "Parameters used to describe centralised config profiles. These should not be edited.", - "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "custom_config_version": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "publish_dir_mode": { "type": "string", - "description": "Git commit id for Institutional configs.", - "default": "master", - "hidden": true, - "fa_icon": "fas fa-users-cog", - "help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```" + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true }, - "custom_config_base": { + "email_on_fail": { "type": "string", - "description": "Base directory for Institutional configs.", - "default": "https://raw.githubusercontent.com/nf-core/configs/master", - "hidden": true, - "help_text": "If you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the `custom_config_base` option. For example:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.", - "fa_icon": "fas fa-users-cog" + "description": "Email address for completion summary, only when pipeline fails.", + "fa_icon": "fas fa-exclamation-triangle", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", + "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.", + "hidden": true + }, + "plaintext_email": { + "type": "boolean", + "description": "Send plain-text email instead of HTML.", + "fa_icon": "fas fa-remove-format", + "hidden": true }, - "hostnames": { + "max_multiqc_email_size": { "type": "string", - "description": "Institutional configs hostname.", - "hidden": true, - "fa_icon": "fas fa-users-cog" + "description": "File size limit when attaching MultiQC reports to summary emails.", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "default": "25.MB", + "fa_icon": "fas fa-file-upload", + "hidden": true }, - "config_profile_description": { + "monochrome_logs": { + "type": "boolean", + "description": "Do not use coloured log outputs.", + "fa_icon": "fas fa-palette", + "hidden": true + }, + "hook_url": { "type": "string", - "description": "Institutional config description.", - "hidden": true, - "fa_icon": "fas fa-users-cog" + "description": "Incoming hook URL for messaging service", + "fa_icon": "fas fa-people-group", + "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.", + "hidden": true }, - "config_profile_contact": { + "multiqc_config": { "type": "string", - "description": "Institutional config contact information.", - "hidden": true, - "fa_icon": "fas fa-users-cog" + "description": "Custom config file to supply to MultiQC.", + "fa_icon": "fas fa-cog", + "hidden": true }, - "config_profile_url": { + "multiqc_logo": { "type": "string", - "description": "Institutional config URL link.", + "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", + "fa_icon": "fas fa-image", + "hidden": true + }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog" + }, + "tracedir": { + "type": "string", + "description": "Directory to keep pipeline Nextflow logs and reports.", + "default": "${params.outdir}/pipeline_info", + "fa_icon": "fas fa-cogs", + "hidden": true + }, + "validate_params": { + "type": "boolean", + "description": "Boolean whether to validate parameters against the schema at runtime", + "default": true, + "fa_icon": "fas fa-check-square", + "hidden": true + }, + "show_hidden_params": { + "type": "boolean", + "fa_icon": "far fa-eye-slash", + "description": "Show all params when using `--help`", "hidden": true, - "fa_icon": "fas fa-users-cog" + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "enable_conda": { + "type": "boolean", + "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", + "hidden": true, + "fa_icon": "fas fa-bacon" } } } @@ -294,19 +293,19 @@ "$ref": "#/definitions/input_output_options" }, { - "$ref": "#/definitions/optimisation_step_options" + "$ref": "#/definitions/optitype_optimisation_steps" }, { "$ref": "#/definitions/reference_genome_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/definitions/institutional_config_options" }, { "$ref": "#/definitions/max_job_request_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..0d62beb --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,10 @@ +# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. +# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. +[tool.black] +line-length = 120 +target_version = ["py37", "py38", "py39", "py310"] + +[tool.isort] +profile = "black" +known_first_party = ["nf_core"] +multi_line_output = 3 diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf new file mode 100644 index 0000000..e24044d --- /dev/null +++ b/subworkflows/local/input_check.nf @@ -0,0 +1,70 @@ +// +// Check input samplesheet and get read channels +// + +include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' + +workflow INPUT_CHECK { + take: + samplesheet // file: /path/to/samplesheet.csv + + main: + SAMPLESHEET_CHECK ( samplesheet ) + .csv + .splitCsv ( header:true, sep:',' ) + .map { create_fastq_channel(it) } + .set { reads } + + emit: + reads // channel: [ val(meta), [ reads ] ] + versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] +} + +// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] +def create_fastq_channel(LinkedHashMap row) { + // create meta map + def meta = [:] + meta.id = row.sample + meta.single_end = row.single_end.toBoolean() + meta.data_type = "fastq" + if (row.seq_type == "dna" || row.seq_type == "rna") { + meta.seq_type = row.seq_type + } + else { + exit 1, "ERROR: Please check input samplesheet -> Invalid sequencing type specified!\n${row.seq_type}" + } + + // add path(s) of the fastq file(s) to the meta map + def bam_provided = ("bam" in row) & (row["bam"] != "") + def fastq_provided = row["fastq_1"] != "" + def fastq_meta = [] + + if (bam_provided & fastq_provided) { + exit 1, "ERROR: Please check input samplesheet -> Please provide fastq OR bam input per samplesheet row!\n${row}" + } + + if(fastq_provided) { + if (!file(row.fastq_1).exists()) { + exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" + } + if (meta.single_end) { + fastq_meta = [ meta, [ file(row.fastq_1) ] ] + } else { + if (!file(row.fastq_2).exists()) { + exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" + } + fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] + } + } + + if (bam_provided) { + if (!file(row.bam).exists()) { + exit 1, "ERROR: Please check input samplesheet -> BAM file does not exist!\n${row.bam}" + } + else { + meta.data_type = "bam" + fastq_meta = [ meta, [ file(row.bam) ] ] + } + } + return fastq_meta +} diff --git a/workflows/hlatyping.nf b/workflows/hlatyping.nf new file mode 100644 index 0000000..1e648a6 --- /dev/null +++ b/workflows/hlatyping.nf @@ -0,0 +1,246 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + VALIDATE INPUTS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) + +// Validate input parameters +WorkflowHlatyping.initialise(params, log) + +// Check input path parameters to see if they exist +def checkPathParamList = [ params.input, params.multiqc_config ] +for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } + +// Check mandatory parameters +if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CONFIG FILES +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT LOCAL MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules +// +include { INPUT_CHECK } from '../subworkflows/local/input_check' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT NF-CORE MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// MODULE: Installed directly from nf-core/modules +// +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { GUNZIP } from '../modules/nf-core/gunzip/main' +include { OPTITYPE } from '../modules/nf-core/optitype/main' +include { CHECK_PAIRED } from '../modules/local/check_paired' +include { SAMTOOLS_COLLATEFASTQ } from '../modules/nf-core/samtools/collatefastq/main' +include { SAMTOOLS_VIEW } from '../modules/nf-core/samtools/view/main' +include { YARA_INDEX } from '../modules/nf-core/yara/index/main' +include { YARA_MAPPER } from '../modules/nf-core/yara/mapper/main' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN MAIN WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// Info required for completion email and summary +def multiqc_report = [] + +workflow HLATYPING { + + ch_versions = Channel.empty() + + // + // SUBWORKFLOW: Read in samplesheet, validate and stage input files + // + INPUT_CHECK ( + ch_input + ) + ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + + // Split by input type (bam/fastq) + INPUT_CHECK.out + .reads + .branch { meta, files -> + bam : meta.data_type == "bam" + fastq : meta.data_type == "fastq" + } + .set { ch_input_files } + + + // determine BAM pairedness for fastq conversion + CHECK_PAIRED (ch_input_files.bam ) + CHECK_PAIRED.out.reads + .map {meta, reads, single_end -> + meta["single_end"] = single_end.text.toBoolean() + [meta, reads] + } + .set { ch_bam_pe_corrected } + ch_versions = ch_versions.mix(CHECK_PAIRED.out.versions) + + + // + // MODULE: Run COLLATEFASTQ + // + SAMTOOLS_COLLATEFASTQ ( + ch_bam_pe_corrected + ) + ch_versions = ch_versions.mix(SAMTOOLS_COLLATEFASTQ.out.versions) + + + // + // Filter for reads depending on pairedness + // + SAMTOOLS_COLLATEFASTQ.out.reads + .map { meta, reads, reads_other, reads_singleton -> + if (meta.single_end) { + [ meta, reads_other ] + } + else { + [meta, reads] + } + } + .set { ch_filtered_bam2fq } + + ch_input_files.fastq + .mix(ch_filtered_bam2fq) + .map { meta, reads -> + [ meta, file("$projectDir/data/references/hla_reference_${meta['seq_type']}.fasta") ] + } + .set { ch_input_with_references } + + + // + // MODULE: Run FastQC + // + FASTQC ( + ch_input_files.fastq + .mix(ch_filtered_bam2fq) + ) + ch_versions = ch_versions.mix(FASTQC.out.versions) + + + // + // MODULE: Run Yara indexing on HLA reference + // + YARA_INDEX ( + ch_input_with_references + ) + ch_versions = ch_versions.mix(YARA_INDEX.out.versions) + + + // + // Map sample-specific reads and index + // + ch_input_files.fastq + .mix(ch_filtered_bam2fq) + .cross(YARA_INDEX.out.index) + .multiMap { reads, index -> + reads: reads + index: index + } + .set { ch_mapping_input } + + + // + // MODULE: Run Yara mapping + // + // Preparation Step - Pre-mapping against HLA + // + // In order to avoid the internal usage of RazerS from within OptiType when + // the input files are of type `fastq`, we perform a pre-mapping step + // here with the `yara` mapper, and map against the HLA reference only. + // + YARA_MAPPER ( + ch_mapping_input.reads, + ch_mapping_input.index + ) + ch_versions = ch_versions.mix(YARA_MAPPER.out.versions) + + + // + // MODULE: OptiType + // + OPTITYPE ( + YARA_MAPPER.out.bam.join(YARA_MAPPER.out.bai) + ) + ch_versions = ch_versions.mix(OPTITYPE.out.versions) + + + // + // MODULE: Pipeline reporting + // + CUSTOM_DUMPSOFTWAREVERSIONS ( + ch_versions.unique().collectFile(name: 'collated_versions.yml') + ) + + + // + // MODULE: MultiQC + // + workflow_summary = WorkflowHlatyping.paramsSummaryMultiqc(workflow, summary_params) + ch_workflow_summary = Channel.value(workflow_summary) + + methods_description = WorkflowHlatyping.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + + ch_multiqc_files = Channel.empty() + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(OPTITYPE.out.output.collect{it[1]}.ifEmpty([])) + + MULTIQC ( + ch_multiqc_files.collect(), + ch_multiqc_config.collect().ifEmpty([]), + ch_multiqc_custom_config.collect().ifEmpty([]), + ch_multiqc_logo.collect().ifEmpty([]), + ) + multiqc_report = MULTIQC.out.report.toList() + ch_versions = ch_versions.mix(MULTIQC.out.versions) + +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + COMPLETION EMAIL AND SUMMARY +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow.onComplete { + if (params.email || params.email_on_fail) { + NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) + } + NfcoreTemplate.summary(workflow, params, log) + if (params.hook_url) { + NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log) + } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/