nf-core/bedtools/coverage @ 0.0.0-6c4ed3a
Summary
computes both the depth and breadth of coverage of features in file B on the features in file A
Get started
Add the following snippet to your workflow script to include this module.
include { BEDTOOLS_COVERAGE } from 'nf-core/bedtools/coverage'
License
MIT License
Process
Name
|
BEDTOOLS_COVERAGE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input_A
file
|
BAM/BED/GFF/VCF file *.{bam,bed,gff,vcf}
|
input_B
file
|
One or more BAM/BED/GFF/VCF file *.{bam,bed,gff,vcf}
|
genome_file
file
|
Optional reference genome 2 column file that defines the expected chromosome order in the input files for use with the -sorted option. When *.{fai,txt,chromsizes}
|
|---|
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bed
file
|
File containing coverage of sequence alignments *.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 powerful toolset for genome arithmetic | https://bedtools.readthedocs.io/en/latest/index.html |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:05:32 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fcoverage/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bedtools/coverage/blobs/sha256:bf46cecbc6c5671c73d7365066c90f683886934e7cf459d2252ae3c19e5e0d3b |
| Size | 2.7 KB |
| Checksum | sha256:bf46cecbc6c5671c73d7365066c90f683886934e7cf459d2252ae3c19e5e0d3b |
| Downloads | 5 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:05:32 (UTC) | 5 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:37 (UTC) | 4 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:46:51 (UTC) | 3 | 2.7 KB |