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update kallistobustools count output list #5110

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8 changes: 5 additions & 3 deletions modules/nf-core/kallistobustools/count/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,11 @@ process KALLISTOBUSTOOLS_COUNT {
val workflow_mode

output:
tuple val(meta), path ("*.count") , emit: count
path "versions.yml" , emit: versions
path "*.count/*/*.mtx" , emit: matrix //Ensure that kallisto finished and produced outputs
tuple val(meta), path ("*.count") , emit: count
tuple val(meta), path ("*.count/counts_unfiltered"), emit: raw_counts
tuple val(meta), path ("*.count/counts_filtered") , emit: filtered_counts, optional: true
path "versions.yml" , emit: versions
path "*.count/*/*.mtx" , emit: matrix //Ensure that kallisto finished and produced outputs

when:
task.ext.when == null || task.ext.when
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8 changes: 8 additions & 0 deletions modules/nf-core/kallistobustools/count/meta.yml
Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,14 @@ output:
type: file
description: kb count output folder
pattern: "*.{count}"
- raw_counts:
type: file
description: kb raw counts output folder
pattern: "*.{count}/counts_unfiltered"
- filtered_counts:
type: file
description: kb filtered counts output folder
pattern: "*.{count}/counts_filtered"
- versions:
type: file
description: File containing software versions
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