Description

Relates methylation calls back to genomic cytosine contexts.

Input

name:type
description
pattern

meta:map

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

coverage_file:file

A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.

meta2:map

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

fasta:file

Reference genome FASTA file

meta3:map

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

index:directory

Bismark genome index directory

BismarkIndex

Output

name:type
description
pattern

coverage

meta:map

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

*.cov.gz:file

A file containing methylation calls per position.

*.cov.gz

report

meta:map

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

*report.txt.gz:file

Genomic cytosine context results.

*report.txt.gz

summary

meta:map

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

*cytosine_context_summary.txt:file

Cyotosine context summary report.

*cytosine_context_summary.txt

versions

versions.yml: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.

github.com/FelixKrueger/Bismark github.com/FelixKrueger/Bismark[...]Docs 10.1093/bioinformatics/btr167
included in
methylseq
maintainers
Github user ewels
Github user sateeshperi
get in touch
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