modules/bamtools_convert

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

bamtoolsbamtools/convertbamconvertbedfastafastqjsonpileupsamyaml

https://github.com/nf-core/modules/[...]/modules/nf-core/bamtools/convert

Description

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

Input

name:type

description

pattern

`meta:map`

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

]

`bam:file`

BAM file

*.bam

Output

name:type

description

pattern

`data`

`meta:map`

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

]

`*.{bed,fasta,fastq,json,pileup,sam,yaml}:file`

Output file

*.{bed,fasta,fastq,json,pileup,sam,yaml}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

bamtools
MIT

C++ API & command-line toolkit for working with BAM data

http://github.com/pezmaster31/bamtools github.com/pezmaster31/bamtools/wiki http://github.com/pezmaster31/bamtools

modules/bamtools_convert

Description

Input

meta:map

bam:file

Output

data

meta:map

*.{bed,fasta,fastq,json,pileup,sam,yaml}:file

versions

versions.yml:file

Tools

bamtools MIT

`meta:map`

`bam:file`

`data`

`meta:map`

`*.{bed,fasta,fastq,json,pileup,sam,yaml}:file`

`versions`

`versions.yml:file`

bamtools
MIT