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

nf-core/bamclipper @ 0.0.0-0c7146d

This module is used to clip primer sequences from your alignments.

primer clipping genomics bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @krannich479

Maintainers: @krannich479

This module is used to clip primer sequences from your alignments.

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

include { BAMCLIPPER } from 'nf-core/bamclipper'

MIT License

Process

`Name`	`BAMCLIPPER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information `[ id:'sample1']`
`bam` file	Sorted BAM file `*.bam`
`bai` file	BAI index of the input BAM file `*.bam.bai`
`bedpe` file	BEDPE file of primer pair locations `*.bed`

Output 4 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information `[ id:'sample1']`
`*.primerclipped.bam.bai` file	BAI index of the output BAM file `*.primerclipped.bam.bai`

#2 bam tuple

`meta` map	Groovy Map containing sample information `[ id:'sample1']`
`*.primerclipped.bam` file	Sorted BAM file containing clipped query sequences according to the given primer pair locations `*.primerclipped.bam`

#3 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

#4 versions_bamclipper tuple

`${task.process}` string	The name of the process
`bamclipper` string	The name of the tool
`1.0.0` string	The hardcoded version of the tool

Tool	Description	Homepage
bamclipper	BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing	https://github.com/tommyau/bamclipper

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:23:40 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbamclipper/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bamclipper/blobs/sha256:612ca9e0a51ebdbabcfede19c4c2b058ed8d04346991d2cdd3be80b088d146eb
Size	2.4 KB
Checksum	sha256:612ca9e0a51ebdbabcfede19c4c2b058ed8d04346991d2cdd3be80b088d146eb
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:23:40 (UTC)		1	2.4 KB	-