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Add cellranger to multiqc report #244

Merged
merged 6 commits into from
Aug 16, 2023
Merged

Add cellranger to multiqc report #244

merged 6 commits into from
Aug 16, 2023

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grst
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@grst grst commented Jun 29, 2023 •
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Since MultiQC v1.15, there's a cellranger module.
This PR activates this functionality for the cellranger branch of the pipeline.

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).

Partly addresses #80

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github-actions bot commented Jun 29, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 8b5707b

+| ✅ 156 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-07 12:10:12

@grst grst requested a review from fmalmeida August 7, 2023 12:10
SPPearce
SPPearce approved these changes Aug 16, 2023
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I have a minor question about what the map is doing, but otherwise all fine.

workflows/scrnaseq.nf
@@ -193,6 +194,9 @@ workflow SCRNASEQ {
ch_versions = ch_versions.mix(CELLRANGER_ALIGN.out.ch_versions)
ch_mtx_matrices = ch_mtx_matrices.mix(CELLRANGER_ALIGN.out.cellranger_out)
ch_star_index = CELLRANGER_ALIGN.out.star_index
ch_multiqc_cellranger = CELLRANGER_ALIGN.out.cellranger_out.map{
meta, outs -> outs.findAll{ it -> it.name == "web_summary.html"}
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Why is this part necessary? Is this something that could be changed in the CELLRANGER_ALIGN module to make it play nicely with multiqc out of the box?

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It's mostly to make MultiQC more efficient, because it only gets the files it needs (the full cellranger output dir contains a lot of files)

@grst grst merged commit 03bf3bf into nf-core:dev Aug 16, 2023
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@SPPearce SPPearce SPPearce approved these changes

@fmalmeida fmalmeida Awaiting requested review from fmalmeida

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@grst @SPPearce