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fix: STAR mtx conversion when using GeneFull #135

Merged
merged 3 commits into from
Jul 31, 2022
Merged

fix: STAR mtx conversion when using GeneFull #135

merged 3 commits into from
Jul 31, 2022

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RHReynolds
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@RHReynolds RHReynolds commented Jul 29, 2022 •
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When STAR is run with the flag --soloFeatures GeneFull (permits
counting of exonic and intronic reads), the output is stored in
*.Solo.out/GeneFull/ and not *.Solo.out/Gene. As a result, matrix
conversion results in an error, as matrix, barcodes and features cannot
be found. This error can be fixed by adding an asterisk in the file
path provided to the mtx conversion modules.

Additionally added compression of starsolo outputs, both for storage
purposes and for downstream compatibility with nf-core/scflow (which
requires gzipped outputs similar to cellranger).

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@RHReynolds
fix: STAR mtx conversion when using GeneFull
370e268 
When STAR is run  with the flag `--soloFeatures GeneFull` (permits
counting of exonic and intronic reads), the output is stored in
`*.Solo.out/GeneFull/` and not `*.Solo.out/Gene`. As a result, matrix
conversion results in an error, as matrix, barcodes and features cannot
be found. This error can be fixed by adding an asterisk in the file
path provided to the mtx conversion modules.
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github-actions bot commented Jul 29, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f15d958

+| ✅ 148 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-29 17:08:45

@RHReynolds RHReynolds marked this pull request as ready for review July 29, 2022 13:40
@RHReynolds
feat: gzip starsolo outputs
f15d958 
Gzipping outputs for file compression and downstream compatibility
with scflow (which requires zipped format, as outputted by cellranger).
fmalmeida
fmalmeida approved these changes Jul 30, 2022
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Looks good to me 😄

@RHReynolds RHReynolds merged commit e106698 into nf-core:dev Jul 31, 2022
@RHReynolds RHReynolds deleted the fix-star-mtx-conversion branch August 9, 2022 14:25
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@fmalmeida fmalmeida fmalmeida approved these changes

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