nf-core/bedtools/shuffle @ 0.0.0-6c4ed3a
Summary
bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file
Get started
Add the following snippet to your workflow script to include this module.
include { BEDTOOLS_SHUFFLE } from 'nf-core/bedtools/shuffle'
License
MIT License
Process
Name
|
BEDTOOLS_SHUFFLE |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing interval information e.g. [ id:'test' ] |
|---|---|
intervals
file
|
Input interval (BED/GFF/VCF) file *.{bed,gff,gff3,vcf}
|
#2
tuple
meta2
map
|
Groovy Map containing genome information e.g. [ id:'test' ] |
|---|---|
chrom_sizes
file
|
Chromosome sizes file *{.genome,.sizes,.txt,.fai}
|
exclude_file
file
|
BED file containing regions to exclude *.{bed}
|
|---|
include_file
file
|
BED file containing regions to include *.{bed}
|
|---|
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing interval information e.g. |
|---|---|
*.bed
file
|
BED file with shuffled intervals *.{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. | n/a |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:05:50 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fshuffle/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bedtools/shuffle/blobs/sha256:5a51150ccb6844b3f490a52523f3725cf127a0a47ff68c2872c5ede30b03316b |
| Size | 3.1 KB |
| Checksum | sha256:5a51150ccb6844b3f490a52523f3725cf127a0a47ff68c2872c5ede30b03316b |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:05:50 (UTC) | 4 | 3.1 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:56 (UTC) | 4 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:47:16 (UTC) | 3 | 3.1 KB |