Description

Merge BAM or CRAM file

Input

name:type
description
pattern

meta:map

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

]

input_files:file

BAM/CRAM file

*.{bam,cram,sam}

meta2:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta:file

Reference file the CRAM was created with (optional)

*.{fasta,fa}

meta3:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fai:file

Index of the reference file the CRAM was created with (optional)

*.fai

Output

name:type
description
pattern

bam

meta:map

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

]

${prefix}.bam:file

BAM file

*.{bam}

cram

meta:map

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

]

${prefix}.cram:file

CRAM file

*.{cram}

csi

meta:map

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

]

*.csi:file

BAM index file (optional)

*.csi

crai

meta:map

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

]

*.crai:file

CRAM index file (optional)

*.crai

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.