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Display a warning when '--extra_star_align_args' are used with RSEM #1049

Merged
merged 2 commits into from
Jun 15, 2023
Merged

Display a warning when '--extra_star_align_args' are used with RSEM #1049

merged 2 commits into from
Jun 15, 2023

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MatthiasZepper
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Since RSEM imposes its own arguments for STAR alignment, custom mapping parameters are not supported for the STAR-RSEM route.

Therefore, --star_extra_alignment_args are silently ignored when the STAR-RSEM route is chosen. As suggested by Thomas Danhorn on Slack, an explicit warning is now displayed to emphasize this.

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>).
  • 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 Jun 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dff30b5

+| ✅ 149 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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: '3.12.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-14 16:23:08

@MatthiasZepper MatthiasZepper self-assigned this Jun 14, 2023
drpatelh
drpatelh reviewed Jun 14, 2023
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drpatelh
drpatelh reviewed Jun 14, 2023
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dff30b5 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
drpatelh
drpatelh approved these changes Jun 15, 2023
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Thanks! 🚀

@drpatelh drpatelh merged commit 6636fcc into nf-core:dev Jun 15, 2023
@MatthiasZepper MatthiasZepper deleted the ExtraStarAlignArgsWarning branch June 22, 2023 10:20
@drpatelh drpatelh changed the title Display a warning when '--star_extra_alignment_args' are used with RSEM Display a warning when '--extra_star_align_args' are used with RSEM Jul 4, 2023
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