nf-core/allelecounter @ 0.0.0-0c7146d
Summary
Generates a count of coverage of alleles
Get started
Add the following snippet to your workflow script to include this module.
include { ALLELECOUNTER } from 'nf-core/allelecounter'
License
MIT License
Process
Name
|
ALLELECOUNTER |
|---|
Input
3 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/SAM index file *.{bai,crai,sai}
|
loci
file
|
loci file *.{tsv}
|
|---|
fasta
file
|
Input genome fasta file. Required when passing CRAM files. |
|---|
Output
2 channels
#1
allelecount
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.alleleCount
file
|
Allele count file *.{alleleCount}
|
#2
versions_allelecounter
tuple
${task.process}
string
|
The name of the process |
|---|---|
alleleCounter
string
|
The name of the tool |
alleleCounter --version
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| allelecounter | Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings) | https://github.com/cancerit/alleleCount |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:21:39 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fallelecounter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/allelecounter/blobs/sha256:5579d343e41a9b04ea50b9372f7b22feb90befc36e46e2935c2dd7fa04a08a72 |
| Size | 2.4 KB |
| Checksum | sha256:5579d343e41a9b04ea50b9372f7b22feb90befc36e46e2935c2dd7fa04a08a72 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:21:39 (UTC) | 1 | 2.4 KB | - |