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add options to stop filtering by PASS #18

Merged
merged 12 commits into from
Nov 22, 2024
Merged

add options to stop filtering by PASS #18

merged 12 commits into from
Nov 22, 2024

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famosab
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@famosab famosab commented Nov 22, 2024 •
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PR checklist

Related to #9

  • 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
  • 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).

We want to stop assuming that everybody just wants the PASS variants in the final MAF file. This is now an optional input :)

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github-actions bot commented Nov 22, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fd07ce6

+| ✅ 158 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config variable not found: validation.help.beforeText
  • nextflow_config - Config variable not found: validation.help.afterText
  • nextflow_config - Config variable not found: validation.summary.beforeText
  • nextflow_config - Config variable not found: validation.summary.afterText
  • nextflow_config - Config manifest.version should end in dev: 1.1.0
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-vcftomaf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/test_full.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-vcftomaf_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/vcftomaf/vcftomaf/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-22 14:59:45

@famosab famosab mentioned this pull request Nov 22, 2024
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@famosab
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famosab commented Nov 22, 2024

Also added the version bump to prepare the next release

@famosab famosab mentioned this pull request Nov 22, 2024
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d4straub
d4straub approved these changes Nov 22, 2024
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LGTM

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Update CHANGELOG.md
fd07ce6 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
FriederikeHanssen
FriederikeHanssen reviewed Nov 22, 2024
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Isn't filtering by PASS much more standard than skipping the filtering?

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famosab commented Nov 22, 2024

Isn't filtering by PASS much more standard than skipping the filtering?

Depends, TCGA never filtered their results by PASS. Usability wise it probably does not matter. Decided to set it to not filter per standard because Leon ran into these issues.
But most people are probably only interested in PASS filtered variants?

@famosab famosab merged commit 3c947e4 into qbic-pipelines:dev Nov 22, 2024
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@famosab famosab deleted the filter branch November 22, 2024 15:06
@FriederikeHanssen
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Isn't filtering by PASS much more standard than skipping the filtering?

Depends, TCGA never filtered their results by PASS. Usability wise it probably does not matter. Decided to set it to not filter per standard because Leon ran into these issues. But most people are probably only interested in PASS filtered variants?

In my experience you just get a ton of noise with the clinical data if you don't filter. This has at least tripped me up many times.

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@famosab @FriederikeHanssen @d4straub