nf-core/hmmcopy/readcounter @ 0.0.0-0c7146d
Summary
readCounter function from HMMcopy utilities, used to generate read in windows
Get started
Add the following snippet to your workflow script to include this module.
include { HMMCOPY_READCOUNTER } from 'nf-core/hmmcopy/readcounter'
License
MIT License
Process
Name
|
HMMCOPY_READCOUNTER |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM file *.{bam,cram}
|
bai
file
|
BAM/CRAM index file *.{bai}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Genome fasta file. Required when using a CRAM file. |
Output
3 channels
#1
wig
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.wig
file
|
A wig file with the number of reads lying within each window in each chromosome *.wig
|
#2
versions_hmmcopy
tuple
${task.process}
string
|
The name of the process |
|---|---|
hmmcopy
string
|
The name of the tool |
0.1.1
string
|
The expression to obtain the version of the tool |
#3
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 |
|---|---|---|
| hmmcopy | C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy | https://github.com/shahcompbio/hmmcopy_utils |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:47:45 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhmmcopy%2Freadcounter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hmmcopy/readcounter/blobs/sha256:b93966f38c60c19c5786291c4c74ea594c5e3b824f23d6bf4d7c1a97c5fcdc0f |
| Size | 2.8 KB |
| Checksum | sha256:b93966f38c60c19c5786291c4c74ea594c5e3b824f23d6bf4d7c1a97c5fcdc0f |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:47:45 (UTC) | 1 | 2.8 KB | - |