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

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

find and mark duplicate reads in BAM file

markduplicates duplicates bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @BioInf2305

Maintainers: @BioInf2305

find and mark duplicate reads in BAM file

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

include { SAMBAMBA_MARKDUP } from 'nf-core/sambamba/markdup'

MIT License

Process

`Name`	`SAMBAMBA_MARKDUP`

Input 1 channel

#1 tuple

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

Output 3 channels

#1 bai tuple

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

#2 bam tuple

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

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
sambamba	process your BAM data faster!	https://lomereiter.github.io/sambamba/docs/sambamba-view.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:27 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsambamba%2Fmarkdup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sambamba/markdup/blobs/sha256:97cadb17131111f830f93ed540c91e012e68b5bfd4385f3743a337a9fe2042a4
Size	2.1 KB
Checksum	sha256:97cadb17131111f830f93ed540c91e012e68b5bfd4385f3743a337a9fe2042a4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:27 (UTC)		1	2.1 KB	-