bam_markduplicates_samtools

Samtools markduplicate SAM/BAM/CRAM file

markdupbamsamcram

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

Description

Samtools markduplicate SAM/BAM/CRAM file

Input

name

description

pattern

`meta`

Groovy Map containing sample information
e.g. [ id:'test' ]

`bam`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`fasta_fai`

FASTA file and index

*.{fasta,fa,fai}

Output

name

description

pattern

`meta`

Groovy Map containing sample information
e.g. [ id:'test' ]

`bam`

Sorted and markduplicate BAM/CRAM/SAM file

*.{bam,cram,sam}