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Add cellrangerarc snippet back #321

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Apr 30, 2024
Merged

Add cellrangerarc snippet back #321

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10 changes: 10 additions & 0 deletions subworkflows/local/mtx_conversion.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,16 @@ workflow MTX_CONVERSION {
main:
ch_versions = Channel.empty()

// Cellranger module output contains too many files which cause path collisions, we filter to the ones we need.
// Keeping backwards compatibility with cellranger-arc.
// TODO: Adapt cellranger-arc subworkflow like cellranger to remove this snippet here.
if (params.aligner in [ 'cellrangerarc' ]) {
mtx_matrices = mtx_matrices.map { meta, mtx_files ->
[ meta, mtx_files.findAll { it.toString().contains("filtered_feature_bc_matrix") } ]
}
.filter { meta, mtx_files -> mtx_files } // Remove any that are missing the relevant files
}

//
// Convert matrix to h5ad
//
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