Description

Performs alignment of BS-Seq reads using bwameth

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

index (dir)

Directory containing bwameth genome index

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Output BAM file containing read alignments

*.{bam}

versions (file)

File containing software versions

versions.yml
included in
methylseq
author
Github user phue
get in touch
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Tools

bwameth
MIT

Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.

github.com/brentp/bwa-meth