Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file

*.bam

Output

name:type
description
pattern

data{:bash}

meta{:bash}

:map

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

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

:file

Output file

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

versions_bamtools{:bash}

${task.process}{:bash}

:string

The name of the process

bamtools{:bash}

:string

The name of the tool

bamtools --version | sed '2!d;s/bamtools //g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bamtools{:bash}

:string

The name of the tool

bamtools --version | sed '2!d;s/bamtools //g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
isoseq
maintainer
Github user sguizard
get in touch
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