modules/dedup

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

dedupdeduplicationpcr duplicatesancient DNApaired-endbam

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

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`
`:map`

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

`bam`
`:file`

BAM/SAM file

*.{bam,sam}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`${prefix}.bam`
`:file`

Deduplicated BAM file

${prefix}.bam

`json`

`meta`
`:map`

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

`${prefix}.json`
`:file`

JSON file for MultiQC

${prefix}.json

`hist`

`meta`
`:map`

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

`${prefix}.hist`
`:file`

Histogram data of amount of deduplication

${prefix}.hist

`log`

`meta`
`:map`

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

`${prefix}.log`
`:file`

Dedup log information

${prefix}.log

`versions_dedup`

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

The name of the process

`dedup`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`dedup`
`:string`

The name of the tool

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

modules/dedup

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`json`

`meta`
`:map`

`${prefix}.json`
`:file`

`hist`

`meta`
`:map`

`${prefix}.hist`
`:file`

`log`

`meta`
`:map`

`${prefix}.log`
`:file`

`versions_dedup`

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

`dedup`
`:string`

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

Topics

`versions`

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

`dedup`
`:string`

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

Tools

dedup
GPL v3

maintainer

get in touch

modules/dedup

Description

Input

meta:map

bam:file

Output

bam

meta:map

${prefix}.bam:file

json

meta:map

${prefix}.json:file

hist

meta:map

${prefix}.hist:file

log

meta:map

${prefix}.log:file

versions_dedup

${task.process}:string

dedup:string

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

Topics

versions

${task.process}:string

dedup:string

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

Tools

dedup GPL v3

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`json`

`meta`
`:map`

`${prefix}.json`
`:file`

`hist`

`meta`
`:map`

`${prefix}.hist`
`:file`

`log`

`meta`
`:map`

`${prefix}.log`
`:file`

`versions_dedup`

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

`dedup`
`:string`

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

`versions`

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

`dedup`
`:string`

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

dedup
GPL v3