Description

CIRCexplorer2 parses fusion junction files from multiple aligners to prepare them for CIRCexplorer2 annotate.

Input

name:type
description
pattern

meta{:bash}

:map

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

fusions{:bash}

:file

BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix.

*.{bam,junction,bed,txt}

Output

name:type
description
pattern

junction{:bash}

meta{:bash}

:map

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

*.bed{:bash}

:file

BED file

*.bed

versions_circexplorer2{:bash}

${task.process}{:bash}

:string

The name of the process

circexplorer2{:bash}

:string

The name of the tool

CIRCexplorer2 --version 2>&1; true{: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

circexplorer2{:bash}

:string

The name of the tool

CIRCexplorer2 --version 2>&1; true{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
circrna
maintainer
Github user BarryDigby
get in touch
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