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Update all nf-core/modules and subworkflows #1330

Merged
merged 15 commits into from
Jun 28, 2024
Merged

Update all nf-core/modules and subworkflows #1330

merged 15 commits into from
Jun 28, 2024

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drpatelh
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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 Jun 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e7ba0cf

+| ✅ 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 2024-06-28 16:04:50

@drpatelh
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Bumping MultiQC version is breaking the pipeline 🤦🏽 I can reproduce locally with the default -profile test

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:MULTIQC'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:MULTIQC` terminated with an error exit status (1)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
      .
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  1

Command output:
  
  /// MultiQC 🔍 v1.22.2
  
              config | Loading config settings from: multiqc_config.yml
              config | Loading config settings from: multiqc_config.yml
         file_search | Only using modules: custom_content, fastqc, cutadapt, fastp, sortmerna, star, hisat2, rsem, salmon, kallisto, samtools, picard, preseq, rseqc, qualimap
         file_search | Search path: /home/harshil/rnaseq/work/61/2a3228af289aec1992dc94b92a5352
              report | Skipping 17 file search patterns
  
      custom_content | biotype_counts: Found 1 samples (bargraph)
                plot | custom_content/custom_content.py: Invalid Heatmap plot configuration {'title': 'DESeq2: Heatmap of the sample-to-sample distances', 'xlab': True, 'reverseColors': True, 'id': 'star_salmon_deseq2_clustering-plot'}:
                plot | • 'xlab': expected type '<class 'str'>', got 'bool' True

Command error:
  Unable to find image 'quay.io/biocontainers/multiqc:1.22.2--pyhdfd78af_0' locally
  1.22.2--pyhdfd78af_0: Pulling from biocontainers/multiqc
  93e509ffbdaf: Already exists
  820c67f471a9: Already exists
  bd9ddc54bea9: Already exists
  eec13b1d39cb: Pulling fs layer
  eec13b1d39cb: Verifying Checksum
  eec13b1d39cb: Download complete
  eec13b1d39cb: Pull complete
  Digest: sha256:99f74ec17286f737c6d01364dcb85df93b86d85471f1ecac8514c1230d7e453a
  Status: Downloaded newer image for quay.io/biocontainers/multiqc:1.22.2--pyhdfd78af_0
  
  /// MultiQC 🔍 v1.22.2
  
              config | Loading config settings from: multiqc_config.yml
              config | Loading config settings from: multiqc_config.yml
         file_search | Only using modules: custom_content, fastqc, cutadapt, fastp, sortmerna, star, hisat2, rsem, salmon, kallisto, samtools, picard, preseq, rseqc, qualimap
         file_search | Search path: /home/harshil/rnaseq/work/61/2a3228af289aec1992dc94b92a5352
              report | Skipping 17 file search patterns
  
      custom_content | biotype_counts: Found 1 samples (bargraph)
                plot | custom_content/custom_content.py: Invalid Heatmap plot configuration {'title': 'DESeq2: Heatmap of the sample-to-sample distances', 'xlab': True, 'reverseColors': True, 'id': 'star_salmon_deseq2_clustering-plot'}:
                plot | • 'xlab': expected type '<class 'str'>', got 'bool' True

@drpatelh
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This PR bumped all of the modules and also had to bump MultiQC to the latest version 1.22.3. I pushed a commit to bring the fields in the custom content in-line with the latest required by MultiQC. However, I still am not seeing any custom content rendered in the MultiQC report - we can fix this in a separate PR.

@pinin4fjords pinin4fjords merged commit a29e775 into nf-core:dev Jun 28, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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@drpatelh @pinin4fjords