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Update nextflow_schema.json #1397

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Update nextflow_schema.json #1397

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@rraadd88 rraadd88 commented Oct 2, 2024

This is a suggestion to clarify the description of the --skip_qc argument. Based on my understanding of the workflow, this argument applies to the stage 4 (post-processing) and 5 (final QC) including DeSeq based QC. I hope this is correct.

Clarification of which QCs are skipped is necessary because steps in stage could also be considered as QC steps. Perhaps a list of skipped QCs would be helpful. For example, I am not sure if --skip_qc skips RSeQC or not.

I hope the documentation for this argument could be more informative.

PR checklist

  • 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/rnaseq 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).

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github-actions bot commented Oct 2, 2024

This PR is against the master branch ❌

  • 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 @rraadd88,

It looks like this pull-request is has been made against the rraadd88/rnaseq-1 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 rraadd88/rnaseq-1 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!

@rraadd88 rraadd88 changed the base branch from master to dev October 2, 2024 15:15
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github-actions bot commented Oct 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 49da4a8

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.16.0
  • 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!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-04 07:52:29

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@rraadd88 @maxulysse