Nextflow Registry | nf-core/dedup@0.0.0-0c7146d

nf-core/dedup @ 0.0.0-0c7146d

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

dedup deduplication pcr duplicates ancient DNA paired-end bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

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

Add the following snippet to your workflow script to include this module.

include { DEDUP } from 'nf-core/dedup'

MIT License

Process

`Name`	`DEDUP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM/SAM file `*.{bam,sam}`

Output 5 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.bam` file	Deduplicated BAM file `${prefix}.bam`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.log` file	Dedup log information `${prefix}.log`

#3 hist tuple

`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`

#4 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.json` file	JSON file for MultiQC `${prefix}.json`

#5 versions_dedup tuple

`${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

Tool	Description	Homepage
dedup	DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).	https://github.com/apeltzer/DeDup

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:34:33 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fdedup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/dedup/blobs/sha256:beef8d69086177d3070919388954974d29104818e5bae9eb42231bbe7fc5d0b1
Size	2.7 KB
Checksum	sha256:beef8d69086177d3070919388954974d29104818e5bae9eb42231bbe7fc5d0b1
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:34:33 (UTC)		1	2.7 KB	-