dhatribadri is testing snakemake workflow 🚀 #98
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test QCD Pipeline | |
| run-name: ${{ github.actor }} is testing snakemake workflow 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Test-QCD-Pipeline: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event." | |
| # - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!" | |
| # - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}." | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner." | |
| - run: echo "🖥️ The workflow is now ready to test your code on the runner." | |
| - name: List files in the repository | |
| run: | | |
| ls | |
| - name: Get working directory | |
| run: | | |
| pwd | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: '3.10' | |
| auto-update-conda: true | |
| activate-environment: 'qcd_env_test' | |
| environment-file: 'qcd_environment.yaml' | |
| use-channel-priority: true | |
| - name: Install pip dependencies | |
| run: | | |
| source $CONDA/bin/activate | |
| conda activate qcd_env_test | |
| pip install --requirement .test/requirements.txt | |
| pip install dropbox | |
| pip install --upgrade tabulate | |
| pip install --upgrade snakemake | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # - name: Install singularity | |
| # uses: eWaterCycle/setup-singularity@v7 | |
| # with: | |
| # singularity-version: 3.8.3 | |
| - name: Install apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.6 | |
| # Download FASTQ files from Dropbox | |
| - name: Download FASTQ files from Dropbox and copy it to local path | |
| env: | |
| DROPBOX_ACCESS_TOKEN: ${{ secrets.DROPBOX_ACCESS_TOKEN }} | |
| run: | | |
| source $CONDA/bin/activate | |
| conda activate qcd_env_test | |
| export DROPBOX_ACCESS_TOKEN=${DROPBOX_ACCESS_TOKEN} | |
| python3 download_fastqs.py | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Create necessary directories | |
| run: | | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/quality_raw | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/trimmomatic | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/raw_coverage | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/spades | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Snakemake workflow | |
| # run: | | |
| # source $CONDA/bin/activate | |
| # conda activate qcd_env_test | |
| # snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: '.' | |
| snakefile: 'QCD.smk' | |
| # install-apptainer: true | |
| task: 'run' | |
| # stagein: 'sudo apt-get install squashfuse fuse2fs gocryptfs' | |
| # stagein: ./mconfig --without-suid && \ | |
| # make -C ./builddir && \ | |
| # make -C ./builddir install | |
| # show-disk-usage-on-error: true | |
| args: '--cores 4 --use-conda --use-apptainer --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000' | |
| #run: echo "🍏 This job's status is ${{ job.status }}." |