Description

Performs alignment of BS-Seq reads using bismark

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)

Bismark genome index directory

BismarkIndex

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}

unmapped (file)

Output FastQ file(s) containing unmapped reads

*.{fq.gz}

report (file)

Bismark alignment reports

*{report.txt}

versions (file)

File containing software versions

versions.yml

Tools

bismark
GPL-3.0-or-later

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.