nf-core/hmmcopy/generatemap @ 0.0.0-0c7146d
Summary
Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
Get started
Add the following snippet to your workflow script to include this module.
include { HMMCOPY_GENERATEMAP } from 'nf-core/hmmcopy/generatemap'
License
MIT License
Process
Name
|
HMMCOPY_GENERATEMAP |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Input genome fasta file |
Output
2 channels
#1
bigwig
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bw
file
|
bigwig file containing the mappability of the genome *.bw
|
#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 |
| 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 18:47:41 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhmmcopy%2Fgeneratemap/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hmmcopy/generatemap/blobs/sha256:ee04b3316507d89659f2b9ca584595d73dbc0442aa95e4edf1807ebe94963933 |
| Size | 2.2 KB |
| Checksum | sha256:ee04b3316507d89659f2b9ca584595d73dbc0442aa95e4edf1807ebe94963933 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:47:41 (UTC) | 1 | 2.2 KB | - |