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Slight fixes for rnaseq preprocessing #1382

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merged 6 commits into from
Sep 16, 2024
Merged

Slight fixes for rnaseq preprocessing #1382

merged 6 commits into from
Sep 16, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Sep 13, 2024 •
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Specifically, this resolves an issue whereby, on a sample failing a trimming check, a string rather than a file would make it into the channel containing input files for multiqc. This would then cause errors like:

Error executing process > 'NFCORE_RNASEQ:RNASEQ:MULTIQC (1)'

Caused by:
  Something went wrong while creating task 'NFCORE_RNASEQ:RNASEQ:MULTIQC' unique id -- Offending keys: [
   - type=java.util.UUID value=e30cfcef-9c41-45b4-885a-a1b5837c20ee, 
   - type=java.lang.String value=NFCORE_RNASEQ:RNASEQ:MULTIQC, 
   - type=java.lang.String value=    def args = task.ext.args ?: ''
      def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
      def config = multiqc_config ? "--config $multiqc_config" : ''
      def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
      def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
      def replace = replace_names ? "--replace-names ${replace_names}" : ''
      def samples = sample_names ? "--sample-names ${sample_names}" : ''
      """
      multiqc \\
          --force \\
          $args \\
          $config \\
          $prefix \\
          $extra_config \\
          $logo \\
          $replace \\
          $samples \\
          .
  
      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
          multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
      END_VERSIONS

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 marked this pull request as draft September 13, 2024 15:47
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github-actions bot commented Sep 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5703690

+| ✅ 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 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 2024-09-16 11:42:54

maxulysse
maxulysse approved these changes Sep 13, 2024
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ok once modules PR is merged

robsyme
robsyme approved these changes Sep 13, 2024
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Tidy, thanks Jon! I'm embarrassed to say I didn't notice the duplicate fail_trimmed_samples_mqc.tsv files when looking through it this morning.

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pinin4fjords commented Sep 16, 2024 •
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Tidy, thanks Jon! I'm embarrassed to say I didn't notice the duplicate fail_trimmed_samples_mqc.tsv files when looking through it this morning.

Not as embarrassed as I am to have duplicated it ;-)

@pinin4fjords pinin4fjords changed the title slight fixes for rnaseq prepro Slight fixes for rnaseq preprocessing Sep 16, 2024
@pinin4fjords pinin4fjords marked this pull request as ready for review September 16, 2024 11:41
@pinin4fjords pinin4fjords merged commit 8def328 into dev Sep 16, 2024
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@pinin4fjords pinin4fjords deleted the rnaseq_propro_trimfail_fix branch September 16, 2024 13:26
@pinin4fjords pinin4fjords mentioned this pull request Sep 16, 2024
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@maxulysse maxulysse maxulysse approved these changes

@robsyme robsyme robsyme approved these changes

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@pinin4fjords @robsyme @maxulysse