umicollapse, index BAM file and run samtools stats, flagstat and idxstats
ch_bam_bai
input BAM file and its index Structure: [ val(meta), path(bam), path(bai) ]
bam
Umi deduplicated BAM/SAM file Structure: [ val(meta), path(bam) ]
index
Umi deduplicated BAM/SAM samtools index (BAI or CSI) Structure: [ val(meta), path(index) ]
dedup_stats
File containing umicollapse deduplication stats Structure: [ val(meta), path(stats) ]
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) ]
