subworkflows/bam_dedup_stats_samtools_umicollapse

umicollapse, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

Description

umicollapse, index BAM file and run samtools stats, flagstat and idxstats

Name (Type)

Description

Pattern

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

Name (Type)

Description

Pattern

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

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

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

File containing umicollapse deduplication stats
Structure: [ val(meta), path(stats) ]

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

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

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

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