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Add outputs for umitools dedup summary stats (#1422)

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Harshil Patel 2022-03-18 20:21:41 +00:00 committed by GitHub
parent 15c7190e22
commit f425aa3cea
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2 changed files with 21 additions and 4 deletions
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7
modules/umitools/dedup/main.nf
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@ -12,6 +12,9 @@ process UMITOOLS_DEDUP {
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*edit_distance.tsv"), emit: tsv_edit_distance
tuple val(meta), path("*per_umi.tsv") , emit: tsv_per_umi
tuple val(meta), path("*per_position.tsv") , emit: tsv_umi_per_position
path "versions.yml" , emit: versions
when:
@ -22,9 +25,11 @@ process UMITOOLS_DEDUP {
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "" : "--paired"
"""
umi_tools dedup \\
umi_tools \\
dedup \\
-I $bam \\
-S ${prefix}.bam \\
--output-stats $prefix \\
$paired \\
$args

12
modules/umitools/dedup/meta.yml
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@ -36,6 +36,18 @@ output:
type: file
description: BAM file with deduplicated UMIs.
pattern: "*.{bam}"
- tsv_edit_distance:
type: file
description: Reports the (binned) average edit distance between the UMIs at each position.
pattern: "*edit_distance.tsv"
- tsv_per_umi:
type: file
description: UMI-level summary statistics.
pattern: "*per_umi.tsv"
- tsv_umi_per_position:
type: file
description: Tabulates the counts for unique combinations of UMI and position.
pattern: "*per_position.tsv"
- versions:
type: file
description: File containing software versions