Description

Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

The input SAM or BAM file to be sorted.

*.{bam,sam}

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

Output SAM or BAM file.

*.{bam,sam}

versions_fgbio{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Tools

fgbio
MIT

Tools for working with genomic and high throughput sequencing data.

github.com/fulcrumgenomics/fgbio http://fulcrumgenomics.github.io/fgbio
maintainer
Github user sruthipsuresh
get in touch
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