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