Description

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

Input

name:type
description
pattern

ch_bam_bai

input BAM file
Structure: [ val(meta), path(bam), path(bai) ]

val_get_dedup_stats :boolean

Generate output stats when running “umi_tools dedup”

Output

name:type
description
pattern

bam

Umi deduplicated BAM/SAM file
Structure: [ val(meta), path(bam) ]

bai

Umi deduplicated BAM/SAM samtools index
Structure: [ val(meta), path(bai) ]

csi

CSI samtools index
Structure: [ val(meta), path(csi) ]

deduplog

UMI-tools deduplication log
Structure: [ val(meta), path(log) ]

stats

File containing samtools stats output
Structure: [ val(meta), path(stats) ]

flagstat

File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]

idxstats

File containing samtools idxstats output
Structure: [ val(meta), path(idxstats) ]

versions

Files containing software versions
Structure: [ path(versions.yml) ]