Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM file

*.{bam,cram}

meta2{:bash}

:map

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

bai{:bash}

:file

BAM/CRAM index file

*.{bai,crai}

meta3{:bash}

:map

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

fasta{:bash}

:file

Input genome fasta file

*.{fasta,fa}

meta4{:bash}

:map

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

fai{:bash}

:file

FASTA index file

*.fai

meta5{:bash}

:map

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

parsed_trim_OT{:bash}

:string

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

meta6{:bash}

:map

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

parsed_trim_OB{:bash}

:string

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

Output

name:type
description
pattern

txt{:bash}

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 containing C->T conversion metrics

*.rastair_call.txt

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 positive C->T conversion as a readout for methylation.

bitbucket.org/bsblabludwig/rastair bitbucket.org/bsblabludwig/rastair/src/master/README.md
maintainer
Github user eduard-casas
get in touch
Ask a question on Slack Open an issue on GitHub