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Merge pull request #1 from getwilds/guidelines-tf
Updating ww-vc-trio to comply with WILDS guidelines
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‎.github/CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at [email protected].
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
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For answers to common questions about this code of conduct, see the FAQ at
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<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
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[homepage]: https://www.contributor-covenant.org

‎.github/CONTRIBUTING.md

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# Contributing
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This outlines how to propose a change to the ww-vc-trio workflow repository.
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For more detailed info about contributing to this, and other WILDS projects, please see the
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[**WILDS Contributing Guide**](https://getwilds.org/guide/).
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## Fixing typos/docs changes
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You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
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## Bigger changes
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If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
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If you’ve found a bug, please file an issue that illustrates the bug with a minimal
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reproducible example.
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### Pull request process
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* Fork the package and clone onto your computer
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* Create a Git branch for your pull request (PR)
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* Make your changes, commit to git, and then create a pull request.
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* The title of your PR should briefly describe the change.
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* The body of your PR should contain `Fixes #issue-number`.
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* For user-facing changes, add a bullet to the changelog file if there is one.
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### Code style
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* New code for WDL repositories should follow our [style guide](https://getwilds.org/guide/wdlconfig.html).
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## Code of Conduct
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Please note that this project is released with a
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[Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this
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project you agree to abide by its terms.

‎.github/ISSUE_TEMPLATE.md

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---
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name: Bug report or feature request
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about: Describe a bug you've seen or make a case for a new feature
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---
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Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, email us at [email protected].
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‎.github/PULL_REQUEST_TEMPLATE.md

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<!--- Provide a general summary of your changes in the Title above -->
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## Description
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<!--- Describe your changes -->
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## Related Issue
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<!--- if this closes an issue make sure include e.g., "fix #4"
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or similar - or if just relates to an issue make sure to mention
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it like "#4" -->
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## Example
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<!--- if introducing a new feature or changing behavior of existing
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methods/functions, include a brief example if possible -->

‎.github/workflows/womtools-validate.yml

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name: WOMtool Validation of WDL Script
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on:
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pull_request:
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types: [opened, reopened, synchronize]
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permissions:
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contents: read
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packages: write
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jobs:
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womtoolval:
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runs-on: ubuntu-latest
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steps:
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-
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name: Checkout
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uses: actions/checkout@v4
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-
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name: Set Up Java
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uses: actions/setup-java@v4
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with:
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distribution: 'temurin'
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java-version: '21'
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-
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name: Pull WOMtool Jarfile
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run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/womtool-86.jar
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-
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name: Validate WDL Scripts
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run: java -jar womtool-86.jar validate *.wdl -i *-inputs.json
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‎README.md

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# ww-vc-trio
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Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
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[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
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This WILDS WDL workflow takes samples through a standard alignment protocol and identifies variants using a trio of well-established variant callers. Finally, the workflow narrows it down to variants of confidence by analyzing consensus amongst the three variant callers.
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## Usage
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For Fred Hutch users that are new to WDL, we recommend using [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this workflow directly to the on-premise HPC cluster, as it simplifies interaction with Cromwell and provides a user-friendly front-end for job submission and tracking. For users outside of Fred Hutch or more advanced users who would like to run the workflow locally, command line execution is relatively straightforward:
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```
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java -jar cromwell-86.jar run ww-vc-trio.wdl \
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--inputs ww-vc-trio-inputs.json \
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--options ww-vc-trio-options.json
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```
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Although Cromwell is demonstrated here, this pipeline is not specific to Cromwell and can be run using whichever WDL execution method you prefer ([miniwdl](https://github.com/chanzuckerberg/miniwdl), [Terra](https://terra.bio/), [HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html), etc.).
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## Support
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For questions, bugs, and/or feature requests, reach out to the Fred Hutch Data Science Lab (DaSL) at [email protected], or open an issue on our [issue tracker](https://github.com/getwilds/ww-vc-trio/issues).
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## Contributing
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If you would like to contribute to this WILDS WDL workflow, see our [contribution guidelines](.github/CONTRIBUTING.md) as well out our [WILDS Contributor Guide](https://getwilds.org/guide/) for more details.
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## License
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Distributed under the MIT License. See `LICENSE` for details.

‎batch_file.tsv

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omics_sample_name molecular_id bamLocation
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TESTDATA TEST /path_to_inputs/smallTestData.unmapped.bam

‎ww-vc-trio-inputs.json

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"ww_vc_trio.af_only_gnomad": "/path_to_references/af-only-gnomad.raw.sites.b37.vcf.gz",
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"ww_vc_trio.af_only_gnomad_index": "/path_to_references/af-only-gnomad.raw.sites.b37.vcf.gz.tbi",
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"ww_vc_trio.annovar_protocols": "refGene,knownGene,cosmic70,esp6500siv2_all,clinvar_20180603,gnomad211_exome",
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"ww_vc_trio.annovar_operation": "g,f,f,f,f,f",
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"ww_vc_trio.githubRepoURL": "https://github.com/FredHutch/tg-wdl-consensusVariants.git",
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"ww_vc_trio.scriptPath": "tg-wdl-consensusVariants/unpaired/consensus-trio.R",
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"ww_vc_trio.githubTag": "v0.1.1"
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"ww_vc_trio.annovar_operation": "g,f,f,f,f,f"
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}

‎ww-vc-trio-options.json

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{
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"workflow_failure_mode": "ContinueWhilePossible",
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"write_to_cache": true,
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"read_from_cache": true,
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"default_runtime_attributes": {
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"maxRetries": 1
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},
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"final_workflow_outputs_dir": "test-output/",
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"use_relative_output_paths": true
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}

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