modules/fgbio_sortbam

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

sortbamsam

https://github.com/nf-core/modules/[...]/modules/nf-core/fgbio/sortbam

Description

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

Input

name:type

description

pattern

`meta:map`

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

`bam:file`

The input SAM or BAM file to be sorted.

*.{bam,sam}

Output

name:type

description

pattern

`bam`

`meta:map`

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

`*.bam:file`

Output SAM or BAM file.

*.{bam,sam}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

fgbio
MIT

Tools for working with genomic and high throughput sequencing data.

github.com/fulcrumgenomics/fgbio http://fulcrumgenomics.github.io/fgbio

modules/fgbio_sortbam

Description

Input

meta:map

bam:file

Output

bam

meta:map

*.bam:file

versions

versions.yml:file

Tools

fgbio MIT

`meta:map`

`bam:file`

`bam`

`meta:map`

`*.bam:file`

`versions`

`versions.yml:file`

fgbio
MIT