Description

Extracts per-base methylation metrics from alignments

Input

name:type
description
pattern

meta:map

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

]

bam:file

BAM/CRAM file

*.{bam,cram}

bai:file

BAM/CRAM index file

*.{bai,crai}

fasta:file

Input genome fasta file

*.{fasta,fa}

fai:file

FASTA index file

*.fai

Output

name:type
description
pattern

bedgraph

meta:map

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

]

*.bedGraph:file

bedGraph file, containing per-base methylation metrics

*.bedGraph

methylkit

meta:map

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

]

*.methylKit:file

methylKit file, containing per-base methylation metrics

*.methylKit

versions

versions.yml:file

File containing software versions

versions.yml

Tools

methyldackel
MIT

Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.