modules/rastair_call

Assess positive C->T conversion as a readout for methylation on a genome-wide basis

methylationrastairC->T conversionbisulphitebisulfitebammCtoT

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

Description

Assess positive C->T conversion as a readout for methylation on a genome-wide 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

`meta5`
`:map`

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

`parsed_trim_OT`
`:string`

Number of nucleotides to trim from Original Top (OT) reads.

`meta6`
`:map`

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

`parsed_trim_OB`
`:string`

Number of nucleotides to trim from Original Bottom (OB) reads.

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.rastair_call.txt`
`:file`

Text file from Rastair call containing C->T conversion metrics

*.rastair_call.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_call

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

`meta5`
`:map`

`parsed_trim_OT`
`:string`

`meta6`
`:map`

`parsed_trim_OB`
`:string`

Output

`txt`

`meta`
`:map`

`*.rastair_call.txt`
`:file`

`versions`

`versions.yml`
`:file`

Tools

rastair
GPL-3.0

included in

maintainer

get in touch

modules/rastair_call

Description

Input

meta:map

bam:file

meta2:map

bai:file

meta3:map

fasta:file

meta4:map

fai:file

meta5:map

parsed_trim_OT:string

meta6:map

parsed_trim_OB:string

Output

txt

meta:map

*.rastair_call.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`

`meta5`
`:map`

`parsed_trim_OT`
`:string`

`meta6`
`:map`

`parsed_trim_OB`
`:string`

`txt`

`meta`
`:map`

`*.rastair_call.txt`
`:file`

`versions`

`versions.yml`
`:file`

rastair
GPL-3.0