Description

Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.

Input

name:type
description
pattern

bam{:bash}

:list

List of Bismark alignment BAM filenames

*.bam

align_report{:bash}

:file

Bismark alignment reports

*report.txt

dedup_report{:bash}

:file

Bismark deduplication reports

*.deduplication_report.txt

splitting_report{:bash}

:file

Bismark splitting reports

*splitting_report.txt

mbias{:bash}

:file

Text file containing methylation bias information

*.txt

Output

name:type
description
pattern

summary{:bash}

*report.{html,txt}{:bash}

:file

Bismark summary

*.{html,txt}

versions_bismark{:bash}

${task.process}{:bash}

:string

The name of the process

bismark{:bash}

:string

The name of the tool

bismark --version 2>&1 | sed -n "s/^.*Bismark Version: v//p" | tr -d "[:space:]"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bismark{:bash}

:string

The name of the tool

bismark --version 2>&1 | sed -n "s/^.*Bismark Version: v//p" | tr -d "[:space:]"{:bash}

:eval

The expression to obtain the version of the tool

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 phue
Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub