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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:09:33 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fhmmcopy%2Freadcounter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hmmcopy/readcounter/blobs/sha256:d54be7f810fe7b15104a65fadaf43f78e68222bd0b98923733f586ae2e0c6850 |
| Size | 2.8 KB |
| Checksum | sha256:d54be7f810fe7b15104a65fadaf43f78e68222bd0b98923733f586ae2e0c6850 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:24:13 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:09:33 (UTC) | 3 | 2.8 KB |