Nextflow Registry | nf-core/bedtools/nuc@0.0.0-0c7146d

nf-core/bedtools/nuc @ 0.0.0-0c7146d

Profiles the nucleotide content of intervals in a fasta file.

bed nucBed bedtools GC content AT content nucleotide content intervals

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @lmfaber

Maintainers: @lmfaber

Summary

Profiles the nucleotide content of intervals in a fasta file.

Get started

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

include { BEDTOOLS_NUC } from 'nf-core/bedtools/nuc'

License

MIT License

Process

`Name`	`BEDTOOLS_NUC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Genome reference `*.{fa,fasta}`
`intervals` file	BED/GFF/VCF file of ranges to extract from -fi `*.{bed,gff,vcf}`

Output 2 channels

#1 bed tuple

meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.bed file

The following information will be reported after each BED entry: %AT content, %GC content, Number of As observed, Number of Cs observed, Number of Gs observed, Number of Ts observed, Number of Ns observed, Number of other bases observed, The length of the explored sequence/interval, The seq. extracted from the FASTA file. (opt., if -seq is used), The number of times a user's pattern was observed. (opt., if -pattern is used.)

*.bed

#2 versions_bedtools tuple

`${task.process}` string	The name of the process
`bedtools` string	The name of the tool
`bedtools --version \| sed -e 's/bedtools v//g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bedtools	A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.	https://bedtools.readthedocs.io

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:26:29 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fnuc/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bedtools/nuc/blobs/sha256:60afe9ecc2b6db55a8510d04aabbe761f46a99095ab41a8e6f0eabcd0ff7bc58
Size	2.7 KB
Checksum	sha256:60afe9ecc2b6db55a8510d04aabbe761f46a99095ab41a8e6f0eabcd0ff7bc58
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:29 (UTC)		1	2.7 KB	-