Skip to content

Commit

Permalink
Merge pull request #321 from nf-core/add-cellrangerarc-snippet-back
Browse files Browse the repository at this point in the history
Add cellrangerarc snippet back
  • Loading branch information
grst authored Apr 30, 2024
2 parents 6a7d203 + 900606f commit 7be5e57
Showing 1 changed file with 10 additions and 0 deletions.
10 changes: 10 additions & 0 deletions subworkflows/local/mtx_conversion.nf
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
//
Expand Down

0 comments on commit 7be5e57

Please sign in to comment.