Nextflow Registry | nf-core/samtools/ampliconclip@0.0.0-0c7146d

nf-core/samtools/ampliconclip @ 0.0.0-0c7146d

Clips read alignments where they match BED file defined regions

amplicon clipping ampliconclip samtools

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @bjohnnyd

Maintainers: @bjohnnyd @matthdsm

Clips read alignments where they match BED file defined regions

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

include { SAMTOOLS_AMPLICONCLIP } from 'nf-core/samtools/ampliconclip'

MIT License

Process

`Name`	`SAMTOOLS_AMPLICONCLIP`

Input 4 channels

#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}`

`bed` file	BED file of regions to be removed (e.g. amplicon primers) `*.{bed}`

`save_cliprejects` boolean	Save filtered reads to a file

`save_clipstats` boolean	Save clipping stats to a file

Output 4 channels

#1 bam tuple

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

#2 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.clipstats.txt` file	Clipping statistics text file `*.{clipstats.txt}`

#3 rejects_bam tuple

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

#4 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

Tool	Description	Homepage
samtools	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:37 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fampliconclip/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/ampliconclip/blobs/sha256:72411739ae9edac7d42887329f06b14752e029bcb77c3ea38fd65ec627077a0e
Size	2.9 KB
Checksum	sha256:72411739ae9edac7d42887329f06b14752e029bcb77c3ea38fd65ec627077a0e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:37 (UTC)		1	2.9 KB	-