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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

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pinin4fjords
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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.

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@pinin4fjords pinin4fjords changed the title Correct conditional for salmon indexing in proprocessing workflow Correct conditional for salmon indexing in preprocessing workflow Aug 15, 2024
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github-actions bot commented Aug 15, 2024 •
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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
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Nice, cleaner code as well.

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

@pinin4fjords
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Thanks all!

@pinin4fjords pinin4fjords merged commit c1809d1 into dev Aug 16, 2024
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@pinin4fjords pinin4fjords deleted the prepro_indexing_fix branch August 16, 2024 08:13
@davidecarlson davidecarlson mentioned this pull request Nov 20, 2024
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@pinin4fjords @davidecarlson @adamrtalbot