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Adding stubs at all level #1335

Merged
merged 42 commits into from
Aug 21, 2024
Merged

Adding stubs at all level #1335

merged 42 commits into from
Aug 21, 2024

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maxulysse
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@maxulysse maxulysse commented Jul 3, 2024 •
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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 Jul 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1b34d1e

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 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
  • 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 2024-08-21 08:20:39

@maxulysse
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hitting:

  -[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)-
  -[nf-core/rnaseq] Please check MultiQC report: 5/5 samples skipped since they failed 10000 trimmed read threshold.-

with stub level pipeline tests...

@maxulysse maxulysse marked this pull request as ready for review July 3, 2024 18:17
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maxulysse commented Jul 4, 2024 •
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Related issues and PRs:

@maxulysse maxulysse mentioned this pull request Jul 8, 2024
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pinin4fjords
pinin4fjords previously approved these changes Jul 11, 2024
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Seems fine to me

@pinin4fjords pinin4fjords added this to the 3.15.0 milestone Jul 11, 2024
This was referenced Jul 16, 2024
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@maxulysse
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New error coming out of Picard:

A field field parsed out of a read name was expected to contain an integer and did not. Read name: SRR6357072.6014972. Cause: String 'SRR6357072.6014972' did not start with a parsable number.

@maxulysse maxulysse mentioned this pull request Jul 22, 2024
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Picard/markduplicates is held back to 3.1.1 due to failing tests at the pipeline level cf #1346

@pinin4fjords pinin4fjords dismissed their stale review August 16, 2024 08:15

Scope has changed since approval

pinin4fjords
pinin4fjords reviewed Aug 20, 2024
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Looking good- couple of lagging points to address. I think we should just point the patched module at the older commit, unless you have a reason that won't work.

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@pinin4fjords pinin4fjords linked an issue Aug 20, 2024 that may be closed by this pull request
Updating picard to 3.2.0 fails pipeline level tests #1346
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pinin4fjords approved these changes Aug 20, 2024
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Looking good, look forward to seeing the snapshotting stuff in a future PR.

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Please update the changelog before any merge

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Please update the changelog before any merge

CHANGELOG updated

@maxulysse maxulysse merged commit ad43736 into nf-core:dev Aug 21, 2024
115 of 120 checks passed
@maxulysse maxulysse deleted the stubs_everywhere branch August 21, 2024 10:04
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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Updating picard to 3.2.0 fails pipeline level tests
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