modules/rastair_mbias

Assess C->T conversion as a readout for methylation on a per-read-position basis.

methylationrastairC->T conversionbisulphitebisulfitebammCtoTmbiasmethylation bias

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

Description

Assess C->T conversion as a readout for methylation on a per-read-position basis.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM file

*.{bam,cram}

`meta2`
`:map`

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

`bai`
`:file`

BAM/CRAM index file

*.{bai,crai}

`meta3`
`:map`

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

`fasta`
`:file`

Input genome fasta file

*.{fasta,fa}

`meta4`
`:map`

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

`fai`
`:file`

FASTA index file

*.fai

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.rastair_mbias.txt`
`:file`

Text file from Rastair mbias containing per-read-position C->T conversion metrics.

*.rastair_mbias.txt

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

rastair
GPL-3.0

A tool for rapid genome-wide assessment of positive C->T conversion as a readout for methylation.

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

modules/rastair_mbias

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

Output

`txt`

`meta`
`:map`

`*.rastair_mbias.txt`
`:file`

`versions`

`versions.yml`
`:file`

Tools

rastair
GPL-3.0

included in

maintainer

get in touch

modules/rastair_mbias

Description

Input

meta:map

bam:file

meta2:map

bai:file

meta3:map

fasta:file

meta4:map

fai:file

Output

txt

meta:map

*.rastair_mbias.txt:file

versions

versions.yml:file

Tools

rastair GPL-3.0

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

`txt`

`meta`
`:map`

`*.rastair_mbias.txt`
`:file`

`versions`

`versions.yml`
`:file`

rastair
GPL-3.0