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

nf-core/umitools/dedup @ 0.0.0-0c7146d

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

umitools deduplication dedup

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @drpatelh @grst @klkeys

Maintainers: @drpatelh @grst @klkeys

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 { UMITOOLS_DEDUP } from 'nf-core/umitools/dedup'

MIT License

Process

`Name`	`UMITOOLS_DEDUP`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM file containing reads to be deduplicated via UMIs. `*.{bam}`
`bai` file	BAM index files corresponding to the input BAM file. `*.{bai}`

`get_output_stats` boolean	Whether or not to generate output stats.

Output 6 channels

#1 bam tuple

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

#3 tsv_per_umi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*per_umi.tsv` file	UMI-level summary statistics. `*per_umi.tsv`

#4 tsv_edit_distance tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*edit_distance.tsv` file	Reports the (binned) average edit distance between the UMIs at each position. `*edit_distance.tsv`

#5 versions_umitools tuple

`${task.process}` string	The name of the process
`umitools` string	The name of the tool
`umi_tools --version \| sed 's/UMI-tools version: //'` eval	The expression to obtain the version of the tool

#6 tsv_umi_per_position tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*per_position.tsv` file	Tabulates the counts for unique combinations of UMI and position. `*per_position.tsv`

Tool	Description	Homepage
umi_tools	UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes	n/a

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:20:44 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fumitools%2Fdedup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/umitools/dedup/blobs/sha256:aad66487b9b344cc9f28ad23f3fb623e35f587efca24b8a36c9eb8d7427bfcdf
Size	3.6 KB
Checksum	sha256:aad66487b9b344cc9f28ad23f3fb623e35f587efca24b8a36c9eb8d7427bfcdf
Downloads	1

Version	Date	Status	Downloads	Size