Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

drpatelh
Copy link
Member

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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jun 20, 2024 •
edited
Loading

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
Copy link
Member Author

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
Copy link
Member Author

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 enabled auto-merge June 27, 2024 15:52
@pinin4fjords pinin4fjords merged commit a29e775 into nf-core:dev Jun 28, 2024
82 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@pinin4fjords pinin4fjords pinin4fjords approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@drpatelh @pinin4fjords