Nextflow Registry | nf-core/samtools/markdup@0.0.0-0c7146d

nf-core/samtools/markdup @ 0.0.0-0c7146d

mark duplicate alignments in a coordinate sorted file

bam duplicates markduplicates samtools

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @priyanka-surana

Maintainers: @priyanka-surana @matthdsm

mark duplicate alignments in a coordinate sorted file

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

include { SAMTOOLS_MARKDUP } from 'nf-core/samtools/markdup'

MIT License

Process

`Name`	`SAMTOOLS_MARKDUP`

Input 2 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference genome file `*.{fa,fasta}`
`fai` file	Reference genome index file `*.fai`

Output 4 channels

#1 bam tuple

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

#2 sam tuple

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

#3 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	CRAM file `*{.cram}`

#4 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
samtools	Tools for dealing with SAM, BAM and CRAM files	http://www.htslib.org

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:10:19 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fmarkdup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/markdup/blobs/sha256:9a4cb4eb46de50bcc5b7d206ee6bb145c35c3410dbe8fd32e0f25775d3de2f6d
Size	2.8 KB
Checksum	sha256:9a4cb4eb46de50bcc5b7d206ee6bb145c35c3410dbe8fd32e0f25775d3de2f6d
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:10:19 (UTC)		1	2.8 KB	-