Skip to content

Slight fixes for rnaseq preprocessing #1382

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
Merged
pinin4fjords merged 6 commits into from
Sep 16, 2024
Merged

Slight fixes for rnaseq preprocessing #1382

pinin4fjords merged 6 commits into from
Sep 16, 2024

Conversation

@pinin4fjords
Copy link
Member

@pinin4fjords pinin4fjords commented Sep 13, 2024 •
edited
Loading

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
@github-actions
Copy link

github-actions bot commented Sep 13, 2024 •
edited
Loading

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
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

ok once modules PR is merged

robsyme
robsyme approved these changes Sep 13, 2024
View reviewed changes
Copy link
Contributor

@robsyme robsyme left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

@pinin4fjords
Copy link
Member Author

pinin4fjords commented Sep 16, 2024 •
edited
Loading

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
@pinin4fjords pinin4fjords deleted the rnaseq_propro_trimfail_fix branch September 16, 2024 13:26
@pinin4fjords pinin4fjords mentioned this pull request Sep 16, 2024
Merged
11 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@robsyme robsyme robsyme approved these changes

@maxulysse maxulysse maxulysse approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

4 participants

@pinin4fjords @robsyme @maxulysse