Description

Concatenate BAM or CRAM file

Input

name:type
description
pattern

meta:map

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

input_files:file

BAM/CRAM files

*.{bam,cram}

Output

name:type
description
pattern

bam

meta:map

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

${prefix}.bam:file

Concatenated BAM file

*.{bam}

cram

meta:map

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

${prefix}.cram:file

Concatenated CRAM file

*.{cram}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.