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{: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{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

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{:bash}`
`:map`

`fusions{:bash}`
`:file`

Output

`junction{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

circexplorer2
MIT License

included in

maintainer

get in touch

modules/circexplorer2_parse

Description

Input

meta{:bash}:map

fusions{:bash}:file

Output

junction{:bash}

meta{:bash}:map

*.bed{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

circexplorer2 MIT License

included in

maintainer

get in touch

`meta{:bash}`
`:map`

`fusions{:bash}`
`:file`

`junction{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

circexplorer2
MIT License