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Fix star index issues #350

Merged
merged 3 commits into from
Aug 12, 2024
Merged

Fix star index issues #350

merged 3 commits into from
Aug 12, 2024

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grst
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@grst grst commented Aug 8, 2024 •
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Close #277
Close #327

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).
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@grst grst changed the base branch from master to dev August 8, 2024 09:07
@nf-core nf-core deleted a comment from github-actions bot Aug 8, 2024
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github-actions bot commented Aug 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ed25fd5

+| ✅ 204 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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 2024-08-12 09:55:44

@grst grst requested a review from fmalmeida August 8, 2024 09:32
nictru
nictru approved these changes Aug 8, 2024
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@nictru nictru left a comment •
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You can do it like this, but alternatively you can use the getGenomeAttribute function and assign the igenomes star index directly to params.star_index like it is done here. This way, you could leave line 70 as it is and params.star_index will always have the correct content.

My proposed approach does not overwrite params.star_index with an igenomes index if it has already been set manually, because nextflow does not allow overwriting parameters.

Will leave this up to you

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grst commented Aug 8, 2024

That's great, wasn't aware of that tooling. I should probably do the same for gtf/fasta then.

@grst grst merged commit 23fcbdb into dev Aug 12, 2024
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@grst grst deleted the fix-star-index branch August 12, 2024 10:02
nictru
nictru reviewed Aug 12, 2024
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workflows/scrnaseq.nf
Comment on lines +70 to +71
star_index = params.star ? file(params.star_index, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('star'), checkIfExists: true ) : [] )
ch_star_index = [[id: star_index.baseName], star_index]
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@nictru nictru Aug 12, 2024 •
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I meant it like this:

params.star_index = getGenomeAttribute('star')
ch_star_index = [[id: star_index.baseName], file(params.star_index, checkIfExists: true)]

You are utilizing params.star which I have not seen elsewhere in the pipeline

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dammit, good catch

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I'll fix it in a separate PR

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@grst grst Aug 12, 2024 •
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params.star_index = getGenomeAttribute('star')

But that logic seems to overwrite params.star_index with the one from iGenomes even when star_index is explicitly set. I find that a bit strange... or am I overlooking something here?

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ah, just saw your edit above now

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That simplifies things

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💯

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Feel free to request my review on a new PR

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@nictru nictru nictru approved these changes

@fmalmeida fmalmeida Awaiting requested review from fmalmeida

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