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Fix: Update variant calling tool - data type table in docs #1635

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Fix: Update variant calling tool - data type table in docs #1635

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famosab
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@famosab famosab commented Aug 28, 2024 •
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PR checklist

Closes #803

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <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).

I updated Normal -> Germline, Tumor -> Tumow-Only, Somatic -> Somatic (Tumor-Normal) to clarify the docs. I changed Strelka to not being able to process tumor-only samples and MSI to being able to process tumor-only.

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github-actions bot commented Aug 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fe06ed9

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-28 13:08:07

@bounlu
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bounlu commented Aug 28, 2024

In the current pipeline, MSIsensorpro doesn't work with tumor-only samples, unless you merge my PR.

@famosab famosab linked an issue Aug 29, 2024 that may be closed by this pull request
Can be tumor-only somatic variant calling performed using Strelka? #803
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@famosab famosab changed the title Update variant calling tool - data type table in docs Fix: Update variant calling tool - data type table in docs Sep 3, 2024
maxulysse
maxulysse reviewed Oct 4, 2024
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docs/usage.md
| [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x |
| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x |
| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x |
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x |
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Suggested change
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x |
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x |

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Not until we merged the PR from @bounlu

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Should we wait for that then?

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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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Can be tumor-only somatic variant calling performed using Strelka?
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@famosab @bounlu @maxulysse