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Fix star index issues #350

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merged 3 commits into from
Aug 12, 2024
Merged

Fix star index issues #350

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d5d3b98
Update CHANGELOG
grst Aug 8, 2024
e6f282d
Merge branch 'dev' into fix-star-index
grst Aug 8, 2024
ed25fd5
Update retrieving star index'
grst Aug 12, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]

- Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
- Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
- Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))

## v2.7.0 - 2024-06-03
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3 changes: 2 additions & 1 deletion workflows/scrnaseq.nf
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Expand Up @@ -67,7 +67,8 @@ workflow SCRNASEQ {
ch_salmon_index = params.salmon_index ? file(params.salmon_index) : []

//star params
ch_star_index = params.star_index ? file(params.star_index) : []
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]
Comment on lines +70 to +71
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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 •
edited
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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

star_feature = params.star_feature

//cellranger params
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