modules/rastair_methylkit

Parses rastair call output and converts it into a MethylKit-compatible format.

methylationrastairC->T conversionbisulphitebisulfitemCtoTmethylkitconvertparser

https://github.com/nf-core/modules/[...]/modules/nf-core/rastair/methylkit

Description

Parses rastair call output and converts it into a MethylKit-compatible format.

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`rastair_call_txt{:bash}`
`:file`

Text file from rastair call

*.rastair_call.txt

Output

name:type

description

pattern

`methylkit{:bash}`

`meta{:bash}`
`:map`

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

`*methylkit.txt.gz{:bash}`
`:file`

Gzipped text file in MethylKit format.

*methylkit.txt.gz

`versions{:bash}`

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

File containing software versions

versions.yml

Tools

rastair
GPL-3.0

A tool for rapid genome-wide assessment of C->T conversion as a readout for methylation. The module uses a script bundled with Rastair to convert formats.

bitbucket.org/bsblabludwig/rastair bitbucket.org/bsblabludwig/rastair/src/master/README.md

modules/rastair_methylkit

Description

Input

`meta{:bash}`
`:map`

`rastair_call_txt{:bash}`
`:file`

Output

`methylkit{:bash}`

`meta{:bash}`
`:map`

`*methylkit.txt.gz{:bash}`
`:file`

`versions{:bash}`

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

Tools

rastair
GPL-3.0

maintainer

get in touch

modules/rastair_methylkit

Description

Input

meta{:bash}:map

rastair_call_txt{:bash}:file

Output

methylkit{:bash}

meta{:bash}:map

*methylkit.txt.gz{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

rastair GPL-3.0

maintainer

get in touch

`meta{:bash}`
`:map`

`rastair_call_txt{:bash}`
`:file`

`methylkit{:bash}`

`meta{:bash}`
`:map`

`*methylkit.txt.gz{:bash}`
`:file`

`versions{:bash}`

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

rastair
GPL-3.0