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fix: STAR mtx conversion when using GeneFull #135

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Jul 31, 2022
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fix: STAR mtx conversion when using GeneFull #135

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370e268
fix: STAR mtx conversion when using GeneFull
RHReynolds Jul 29, 2022
09b9f63
docs: update changelog
RHReynolds Jul 29, 2022
f15d958
feat: gzip starsolo outputs
RHReynolds Jul 29, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixes

- Fixed Kallistobustools workflow [#123](https://github.com/nf-core/scrnaseq/issues/123) by upgrading to nf-core/modules module
- Fixed matrix conversion error when running STAR with --soloFeatures GeneFull [#135](https://github.com/nf-core/scrnaseq/pull/135)

## v2.0.0 - 2022-06-17 "Gray Nickel Beagle"

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6 changes: 3 additions & 3 deletions modules/local/mtx_to_h5ad.nf
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Expand Up @@ -26,9 +26,9 @@ process MTX_TO_H5AD {
barcodes_tsv = "*_alevin_results/alevin/quants_mat_rows.txt"
features_tsv = "*_alevin_results/alevin/quants_mat_cols.txt"
} else if (params.aligner == 'star') {
mtx_matrix = "*.Solo.out/Gene/filtered/matrix.mtx"
barcodes_tsv = "*.Solo.out/Gene/filtered/barcodes.tsv"
features_tsv = "*.Solo.out/Gene/filtered/features.tsv"
mtx_matrix = "*.Solo.out/Gene*/filtered/matrix.mtx.gz"
barcodes_tsv = "*.Solo.out/Gene*/filtered/barcodes.tsv.gz"
features_tsv = "*.Solo.out/Gene*/filtered/features.tsv.gz"
}

//
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6 changes: 3 additions & 3 deletions modules/local/mtx_to_seurat.nf
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Expand Up @@ -30,9 +30,9 @@ process MTX_TO_SEURAT {
barcodes = "*_alevin_results/alevin/quants_mat_rows.txt"
features = "*_alevin_results/alevin/quants_mat_cols.txt"
} else if (params.aligner == 'star') {
matrix = "*.Solo.out/Gene/filtered/matrix.mtx"
barcodes = "*.Solo.out/Gene/filtered/barcodes.tsv"
features = "*.Solo.out/Gene/filtered/features.tsv"
matrix = "*.Solo.out/Gene*/filtered/matrix.mtx.gz"
barcodes = "*.Solo.out/Gene*/filtered/barcodes.tsv.gz"
features = "*.Solo.out/Gene*/filtered/features.tsv.gz"
}

"""
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5 changes: 5 additions & 0 deletions modules/local/star_align.nf
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Expand Up @@ -69,6 +69,11 @@ process STAR_ALIGN {
gzip ${prefix}.unmapped_2.fastq
fi

if [ -d ${prefix}.Solo.out ]; then
# Backslashes still need to be escaped (https://github.com/nextflow-io/nextflow/issues/67)
find ${prefix}.Solo.out \\( -name "*.tsv" -o -name "*.mtx" \\) -exec gzip {} \\;
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
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