Description

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

Input

name:type
description
pattern

ch_reads

Sequence reads in BAM/CRAM/SAM format
Structure: [ val(meta), path(reads) ]

ch_fasta

Reference genome fasta file required for CRAM input
Structure: [ path(fasta) ]

ch_fasta

Index of the reference genome fasta file
Structure: [ path(fai) ]

Output

name:type
description
pattern

bam

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

bai

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

cram

processed CRAM file
Structure: [ val(meta), path(cram) ]

crai

CRAM samtools index
Structure: [ val(meta), path(crai) ]

csi

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

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) ]