nf-core/jvarkit/wgscoverageplotter @ 0.0.0-0c7146d
Summary
Plot whole genome coverage from BAM/CRAM file as SVG
Get started
Add the following snippet to your workflow script to include this module.
include { JVARKIT_WGSCOVERAGEPLOTTER } from 'nf-core/jvarkit/wgscoverageplotter'
License
MIT License
Process
Name
|
JVARKIT_WGSCOVERAGEPLOTTER |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
bam
file
|
BAM/CRAM file from alignment *.{bam,cram}
|
bai
file
|
BAI/CRAI file from alignment *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'test_reference' ] |
|---|---|
fasta
file
|
The reference fasta file *.fasta
|
#3
tuple
meta3
map
|
Groovy Map containing reference fai information e.g. [ id:'test_reference' ] |
|---|---|
fai
file
|
Index of reference fasta file fasta.fai
|
#4
tuple
meta4
map
|
Groovy Map containing reference dict information e.g. [ id:'test_reference' ] |
|---|---|
dict
file
|
GATK sequence dictionary *.dict
|
Output
2 channels
#1
output
tuple
meta
map
|
Groovy Map containing Sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.svg
file
|
Output SVG file *.svg
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| jvarkit | Java utilities for Bioinformatics. | https://github.com/lindenb/jvarkit |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:12:23 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fwgscoverageplotter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jvarkit/wgscoverageplotter/blobs/sha256:5bc6a03ebd4e259d4805fda7054053ac6e9711211985faa8e17a6480ce5a07a4 |
| Size | 2.5 KB |
| Checksum | sha256:5bc6a03ebd4e259d4805fda7054053ac6e9711211985faa8e17a6480ce5a07a4 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:31 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:29 (UTC) | 3 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:23 (UTC) | 3 | 2.5 KB |