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Reinstate pseudoalignment subworkflow config #1310

Merged
merged 4 commits into from
Jun 18, 2024
Merged

Reinstate pseudoalignment subworkflow config #1310

merged 4 commits into from
Jun 18, 2024

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pinin4fjords
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We have inadvertently orphaned the psuedoalignment subworkflow's config (since it was moved from the old config/modules.conf). Reinstating it here so that e.g. 'extra_salmon_quant_args' is passed.

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).

@pinin4fjords pinin4fjords added this to the 3.15.0 milestone May 30, 2024
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github-actions bot commented May 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ef7fc82

+| ✅ 171 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-18 11:07:08

@pinin4fjords
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Thanks @FriederikeHanssen !

@pinin4fjords pinin4fjords merged commit fa34ca6 into dev Jun 18, 2024
185 checks passed
@pinin4fjords pinin4fjords deleted the fix_salmon_args branch June 18, 2024 13:59
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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