Description

Replace the header in the bam file with the header generated by the command. This command is much faster than replacing the header with a BAM→SAM→BAM conversion.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM file to be reheaded

*.{bam,cram}

bai{:bash}

:file

BAM/CRAM index file to be reheaded

*.{bai,crai,csi}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Reheaded BAM/CRAM file

*.{bam,cram}

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The command used to generate the version of the tool

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.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
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maintainers
Github user louislenezet
Github user matthdsm
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