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add paths in output directive in cellranger cout module #5108

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merged 5 commits into from
Mar 18, 2024
Merged

add paths in output directive in cellranger cout module #5108

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c2825b1
add paths in output directive
fmalmeida Mar 13, 2024
c01cae7
update meta.yml
fmalmeida Mar 13, 2024
8023539
add stub file generation
fmalmeida Mar 18, 2024
4fc08d2
also create fake files in new stub
fmalmeida Mar 18, 2024
a7ce968
update stub snaps as new output channels are now emitted
fmalmeida Mar 18, 2024
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6 changes: 4 additions & 2 deletions modules/nf-core/cellranger/count/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,10 @@ process CELLRANGER_COUNT {
path reference

output:
tuple val(meta), path("**/outs/**"), emit: outs
path "versions.yml" , emit: versions
tuple val(meta), path("**/outs/**") , emit: outs
tuple val(meta), path("**/outs/filtered_feature_bc_matrix**"), emit: filtered
tuple val(meta), path("**/outs/raw_feature_bc_matrix**") , emit: raw
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
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8 changes: 8 additions & 0 deletions modules/nf-core/cellranger/count/meta.yml
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Expand Up @@ -40,6 +40,14 @@ output:
type: file
description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
pattern: "${meta.id}/outs/*"
- filtered:
type: file
description: Files containing the filtered outputs of Cell Ranger.
pattern: "**/outs/filtered_feature_bc_matrix**"
- raw:
type: file
description: Files containing the raw outputs of Cell Ranger.
pattern: "**/outs/raw_feature_bc_matrix**"
- versions:
type: file
description: File containing software version
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