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

Correct conditional for salmon indexing in preprocessing workflow #1353

Merged
merged 2 commits into from
Aug 16, 2024
Merged

Correct conditional for salmon indexing in preprocessing workflow #1353

merged 2 commits into from
Aug 16, 2024

Conversation

pinin4fjords
Copy link
Member

As reported by @davidecarlson. In certain circumstances the workflow would complete prior to running Salmon for strandedness detection in preprocessing. I figured out that this was due to an emtpy ch_index channel for Salmon in that subworkflow, and it was empty due to errors in conditional logic at the workflow level

Specifically this occurred when:

  1. An 'auto' was set in the sample sheet, necessitating a Salmon run and consequently a Salmon index
  2. A Salmon index hadn't otherwise been created (e.g. where pseudo-aligner had been set to 'Salmon').

The fix is to correct the conditional logic such that ad-hoc index is requested correctly.

The subworkflow can't condition its structure on the possibility of an empty index channel, since that is not known until run time- hence the need for this explicit boolean based on input parameters.

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 changed the title Correct conditional for salmon indexing in proprocessing workflow Correct conditional for salmon indexing in preprocessing workflow Aug 15, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Aug 15, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0e6d601

+| ✅ 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 2024-08-15 16:19:33

adamrtalbot
adamrtalbot approved these changes Aug 15, 2024
View reviewed changes
Copy link
Contributor

@adamrtalbot adamrtalbot left a comment

Choose a reason for hiding this comment

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

Nice, cleaner code as well.

@davidecarlson
Copy link

I tested this branch of the pipeline and can confirm that these changes fixed the issue I reported. Thanks for that!

@pinin4fjords
Copy link
Member Author

Thanks all!

@pinin4fjords pinin4fjords merged commit c1809d1 into dev Aug 16, 2024
25 checks passed
@pinin4fjords pinin4fjords deleted the prepro_indexing_fix branch August 16, 2024 08:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@adamrtalbot adamrtalbot adamrtalbot 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.
3 participants
@pinin4fjords @davidecarlson @adamrtalbot