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Published 20 hours ago • verified publisher icon nf-core

Adding stubs at all level

Open maxulysse opened this issue 1 year ago • 3 comments

  • No stubs for utils_* subworkflows (local or from nf-core as no process so no stubs).
  • modules/local:
    • https://github.com/nf-core/rnaseq/pull/1331
  • modules/nf-core:
    • https://github.com/nf-core/modules/pull/5854
    • https://github.com/nf-core/modules/pull/5861
  • subworkflows/local:
    • This current PR
  • subworkflows/nf-core:
    • https://github.com/nf-core/modules/pull/5911
    • https://github.com/nf-core/modules/pull/5913
    • https://github.com/nf-core/modules/pull/5921
    • https://github.com/nf-core/modules/pull/5922
  • pipeline:
    • This current PR, with a crude implementation

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).

maxulysse avatar Jul 03 '24 09:07 maxulysse

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 1b34d1e

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

:heavy_exclamation_mark: 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

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-21 08:20:39

github-actions[bot] avatar Jul 03 '24 09:07 github-actions[bot]

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 avatar Jul 03 '24 18:07 maxulysse

Related issues and PRs:

  • https://github.com/nf-core/tools/issues/3049
  • https://github.com/nf-core/website/pull/2621

maxulysse avatar Jul 04 '24 09:07 maxulysse

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 avatar Jul 22 '24 08:07 maxulysse

Picard/markduplicates is held back to 3.1.1 due to failing tests at the pipeline level cf https://github.com/nf-core/rnaseq/issues/1346

maxulysse avatar Jul 22 '24 18:07 maxulysse

Please update the changelog before any merge

pinin4fjords avatar Aug 20 '24 14:08 pinin4fjords

Please update the changelog before any merge

CHANGELOG updated

maxulysse avatar Aug 21 '24 08:08 maxulysse