Description

Merge split bam/sam chunks in one file

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

bam:file

List of BAM/SAM chunks to merge

*.{bam,sam}

Output

name:type
description
pattern

bam

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

output/**.{bam,sam}:file

Merged BAM/SAM file

*.{bam,sam}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

elprep
AGPL v3

elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.