modules/circexplorer2_parse

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

parsecircrnasplice

https://github.com/nf-core/modules/[...]/modules/nf-core/circexplorer2/parse

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`fusions`
`: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`

`meta`
`:map`

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

`*.bed`
`:file`

BED file

*.bed

`versions_circexplorer2`

`${task.process}`
`:string`

The name of the process

`circexplorer2`
`:string`

The name of the tool

`CIRCexplorer2 --version 2>&1; true`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`circexplorer2`
`:string`

The name of the tool

`CIRCexplorer2 --version 2>&1; true`
`:eval`

The expression to obtain the version of the tool

Tools

circexplorer2
MIT License

Circular RNA analysis toolkit

github.com/YangLab/CIRCexplorer2 circexplorer2.readthedocs.io/en/latest 10.1101/gr.202895.115

modules/circexplorer2_parse

Description

Input

`meta`
`:map`

`fusions`
`:file`

Output

`junction`

`meta`
`:map`

`*.bed`
`:file`

`versions_circexplorer2`

`${task.process}`
`:string`

`circexplorer2`
`:string`

`CIRCexplorer2 --version 2>&1; true`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`circexplorer2`
`:string`

`CIRCexplorer2 --version 2>&1; true`
`:eval`

Tools

circexplorer2
MIT License

included in

maintainer

get in touch

modules/circexplorer2_parse

Description

Input

meta:map

fusions:file

Output

junction

meta:map

*.bed:file

versions_circexplorer2

${task.process}:string

circexplorer2:string

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

Topics

versions

${task.process}:string

circexplorer2:string

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

Tools

circexplorer2 MIT License

included in

maintainer

get in touch

`meta`
`:map`

`fusions`
`:file`

`junction`

`meta`
`:map`

`*.bed`
`:file`

`versions_circexplorer2`

`${task.process}`
`:string`

`circexplorer2`
`:string`

`CIRCexplorer2 --version 2>&1; true`
`:eval`

`versions`

`${task.process}`
`:string`

`circexplorer2`
`:string`

`CIRCexplorer2 --version 2>&1; true`
`:eval`

circexplorer2
MIT License