modules/bismark_deduplicate

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

bismark3-letter genomemapmethylation5mCmethylseqbisulphitebisulfitebam

https://github.com/nf-core/modules/[...]/modules/nf-core/bismark/deduplicate

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file containing read alignments

*.{bam}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.deduplicated.bam`
`:file`

Deduplicated output BAM file containing read alignments

*.{deduplicated.bam}

`report`

`meta`
`:map`

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

`*.deduplication_report.txt`
`:file`

Bismark deduplication reports

*.{deduplication_report.txt}

`versions_bismark`

`${task.process}`
`:string`

The name of the process

`bismark`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`bismark`
`:string`

The name of the tool

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

modules/bismark_deduplicate

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`bam`

`meta`
`:map`

`*.deduplicated.bam`
`:file`

`report`

`meta`
`:map`

`*.deduplication_report.txt`
`:file`

`versions_bismark`

`${task.process}`
`:string`

`bismark`
`:string`

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

Topics

`versions`

`${task.process}`
`:string`

`bismark`
`:string`

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

Tools

bismark
GPL-3.0-or-later

included in

maintainers

get in touch

modules/bismark_deduplicate

Description

Input

meta:map

bam:file

Output

bam

meta:map

*.deduplicated.bam:file

report

meta:map

*.deduplication_report.txt:file

versions_bismark

${task.process}:string

bismark:string

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

Topics

versions

${task.process}:string

bismark:string

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

Tools

bismark GPL-3.0-or-later

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bam`

`meta`
`:map`

`*.deduplicated.bam`
`:file`

`report`

`meta`
`:map`

`*.deduplication_report.txt`
`:file`

`versions_bismark`

`${task.process}`
`:string`

`bismark`
`:string`

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

`versions`

`${task.process}`
`:string`

`bismark`
`:string`

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

bismark
GPL-3.0-or-later