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Ensure that starsolo outputs channel that matches others, including meta map #220

Merged
merged 4 commits into from
May 2, 2023
Merged

Ensure that starsolo outputs channel that matches others, including meta map #220

merged 4 commits into from
May 2, 2023

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robsyme
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@robsyme robsyme commented Apr 27, 2023 •
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Overview

Before this PR, the STARSOLO local subworkflow emits the for_multiqc channel and in doing so trims out the meta map by returning just the path with .collect{it[1]}:

    emit:
    // snip
    for_multiqc = STAR_ALIGN.out.log_final.collect{it[1]}.ifEmpty([])

This for_multiqc output is then assigned to ch_multiqc_star:

ch_multiqc_star = STARSOLO.out.for_multiqc

and then imported into multiqc, but in doing so assumes that the meta map is still included, and re-trims it:

ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{it[1]}.ifEmpty([]))

Performing two rounds of .collect{it[1]} returns a null object, which throws an error when MultiQC is queued.

The Fix

I removed the first meta map removal in the STARSOLO subworkflow.

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/scrnaseq 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>).
  • 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 Apr 27, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 4f393da

+| ✅ 158 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-28 17:55:45

@robsyme robsyme marked this pull request as ready for review April 28, 2023 16:41
@robsyme robsyme requested a review from apeltzer April 28, 2023 16:56
@robsyme robsyme enabled auto-merge April 30, 2023 18:28
ggabernet
ggabernet approved these changes May 2, 2023
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Looks good to me!

@robsyme robsyme merged commit be53837 into dev May 2, 2023
@robsyme robsyme deleted the null-path-fix branch May 2, 2023 02:19
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@ggabernet ggabernet ggabernet approved these changes

@apeltzer apeltzer Awaiting requested review from apeltzer

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@robsyme @ggabernet