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

nf-core/umicollapse @ 0.0.0-0c7146d

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

umicollapse deduplication genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @CharlotteAnne @chris-cheshire

Maintainers: @CharlotteAnne @chris-cheshire @apeltzer @siddharthab @MatthiasZepper

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

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

include { UMICOLLAPSE } from 'nf-core/umicollapse'

MIT License

Process

`Name`	`UMICOLLAPSE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	Input bam file `*.bam`
`bai` file	BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input. `*.{bai}`

`mode` string	Selects the mode of Umicollapse - either fastq or bam need to be provided. `{fastq,bam}`

Output 4 channels

#1 bam tuple

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

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_UMICollapse.log` file	A log file with the deduplication statistics. `*_{UMICollapse.log}`

#3 fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`dedupfastq.gz` file	FASTQ file with deduplicated UMIs. `dedupfastq.gz`

#4 versions_umicollapse tuple

`${task.process}` string	The name of the process
`umicollapse` string	The name of the tool
`1.1.0-0` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
umicollapse	UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).	https://github.com/Daniel-Liu-c0deb0t/UMICollapse

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:20:42 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fumicollapse/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/umicollapse/blobs/sha256:4cac0a44acc17214f96fb822de4c0d59af9ee2416218c548faebdebe4d4a561f
Size	3.7 KB
Checksum	sha256:4cac0a44acc17214f96fb822de4c0d59af9ee2416218c548faebdebe4d4a561f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:20:42 (UTC)		1	3.7 KB	-