Description

DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/SAM file

*.{bam,sam}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

Deduplicated BAM file

${prefix}.bam

json{:bash}

meta{:bash}

:map

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

${prefix}.json{:bash}

:file

JSON file for MultiQC

${prefix}.json

hist{:bash}

meta{:bash}

:map

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

${prefix}.hist{:bash}

:file

Histogram data of amount of deduplication

${prefix}.hist

log{:bash}

meta{:bash}

:map

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

${prefix}.log{:bash}

:file

Dedup log information

${prefix}.log

versions_dedup{:bash}

${task.process}{:bash}

:string

The name of the process

dedup{:bash}

:string

The name of the tool

dedup --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+'{: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

dedup{:bash}

:string

The name of the tool

dedup --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+'{:bash}

:eval

The expression to obtain the version of the tool

Tools

dedup
GPL v3

DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).

github.com/apeltzer/DeDup dedup.readthedocs.io/en/latest https://github.com/apeltzer/DeDup 10.1186/s13059-016-0918-z
maintainer
Github user jfy133
get in touch
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