Nextflow Registry | nf-core/bedtools/nuc@0.0.0-6c4ed3a

nf-core/bedtools/nuc @ 0.0.0-6c4ed3a

Profiles the nucleotide content of intervals in a fasta file.

bed nucBed bedtools GC content AT content nucleotide content intervals

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:05:48 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fnuc/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bedtools/nuc/blobs/sha256:89d45c8974adccb12db63dc3c848b71727c0e913af27e7896e91c3643ab3075e
Size	2.7 KB
Checksum	sha256:89d45c8974adccb12db63dc3c848b71727c0e913af27e7896e91c3643ab3075e
Downloads	4

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:05:48 (UTC)	4	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:03:53 (UTC)	3	2.7 KB
0.0.0-0c7146d	08 Apr 2026 18:47:13 (UTC)	3	2.7 KB