nf-core/bedtools/map @ 0.0.0-3fc6d40
Summary
Allows one to screen for overlaps between two sets of genomic features.
Get started
Add the following snippet to your workflow script to include this module.
include { BEDTOOLS_MAP } from 'nf-core/bedtools/map'
License
MIT License
Process
Name
|
BEDTOOLS_MAP |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
intervals1
file
|
BAM/BED/GFF/VCF *.{bed|gff|vcf}
|
intervals2
file
|
BAM/BED/GFF/VCF *.{bed|gff|vcf}
|
#2
tuple
meta2
map
|
Groovy Map containing reference chromosome sizes e.g. [ id:'test' ] |
|---|---|
chrom_sizes
file
|
Chromosome sizes file *{.sizes,.txt}
|
Output
2 channels
#1
mapped
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.${extension}
file
|
File containing the description of overlaps found between the features in A and the features in B, with statistics *.${extension}
|
#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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:03:47 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fmap/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bedtools/map/blobs/sha256:fc60750320ac0d849d441df0054bc64b841ef50e995f309ff8de729dc7e7b4ed |
| Size | 2.6 KB |
| Checksum | sha256:fc60750320ac0d849d441df0054bc64b841ef50e995f309ff8de729dc7e7b4ed |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:05:42 (UTC) | 5 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:47 (UTC) | 4 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:47:05 (UTC) | 4 | 2.6 KB |