bam_markduplicates_picard

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

markduplicatesbamsamcram

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_markduplicates_picard

Description

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

Input

name

description

pattern

`ch_reads`

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

`ch_fasta_fai`

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

Output

name

description

pattern

`bam`

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

`cram`

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

`metrics`

Duplicate metrics file generated by Picard MarkDuplicates
Structure: [ val(meta), path(metrics) ]

`index`

BAM/CRAM samtools index (bai, crai or csi)
Structure: [ val(meta), path(index) ]

`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) ]

`per_sample_mqc_bundle`

Per-sample MultiQC-feeding outputs (stats, flagstat, idxstats, metrics) joined on meta.
Structure: [ val(meta), list(files) ]