Nextflow Registry | nf-core/bamutil/clipoverlap@0.0.0-0c7146d

nf-core/bamutil/clipoverlap @ 0.0.0-0c7146d

clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.

bam clipping clipOverlap bamUtil

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Y-Pei

Maintainers: @Y-Pei

clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.

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

include { BAMUTIL_CLIPOVERLAP } from 'nf-core/bamutil/clipoverlap'

MIT License

Process

`Name`	`BAMUTIL_CLIPOVERLAP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bam` file	Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file `*.{bam,sam,ubam}`

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bam` file	Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file `*.{bam}`

#2 stats_log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	basic overlap statistics when unabled with --stats `*.{log}`

#3 versions_bamutil tuple

`${task.process}` string	The name of the process
`bamutil` string	The name of the tool
`bam clipOverlap 2>&1 \| grep '^Version:' \| sed 's/^Version: //;s/;.*//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bamutil	Programs that perform operations on SAM/BAM files, all built into a single executable, bam.	https://genome.sph.umich.edu/wiki/BamUtil

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:24:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbamutil%2Fclipoverlap/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bamutil/clipoverlap/blobs/sha256:2bb2c34352b3cc6ea0e9f366e730fa0055b9bf31be332e72b03bbf50d6f459ef
Size	2.5 KB
Checksum	sha256:2bb2c34352b3cc6ea0e9f366e730fa0055b9bf31be332e72b03bbf50d6f459ef
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:24:25 (UTC)		1	2.5 KB	-