Description

Removes alignments to the same position in the genome from the Bismark mapping output.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file containing read alignments

*.{bam}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.deduplicated.bam{:bash}

:file

Deduplicated output BAM file containing read alignments

*.{deduplicated.bam}

report{:bash}

meta{:bash}

:map

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

*.deduplication_report.txt{:bash}

:file

Bismark deduplication reports

*.{deduplication_report.txt}

versions_bismark{:bash}

${task.process}{:bash}

:string

The name of the process

bismark{:bash}

:string

The name of the tool

bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'{: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 -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'{: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