nf-core/samtools/coverage @ 0.0.0-6c4ed3a
Summary
produces a histogram or table of coverage per chromosome
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_COVERAGE } from 'nf-core/samtools/coverage'
License
MIT License
Process
Name
|
SAMTOOLS_COVERAGE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
input_index
file
|
BAM/CRAM index file *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
Reference genome file *.{fa,fasta}
|
fai
file
|
Reference genome index file *.fai
|
Output
2 channels
#1
coverage
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram). *.txt
|
#2
versions_samtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
samtools
string
|
The name of the tool |
samtools version | sed '1!d;s/.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. | http://www.htslib.org/ |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:42:14 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fcoverage/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/coverage/blobs/sha256:50a4f96ccb1394363622b6bd29ad7121ac1f774c1623dde600f9875191057c28 |
| Size | 3.0 KB |
| Checksum | sha256:50a4f96ccb1394363622b6bd29ad7121ac1f774c1623dde600f9875191057c28 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:42:14 (UTC) | 4 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:34 (UTC) | 3 | 3.0 KB |