nf-core/allelecounter @ 0.0.0-3fc6d40
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:01:29 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fallelecounter/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/allelecounter/blobs/sha256:306011553f9ff32f6120f8b8b0695b109e89175dbde36a6ee31f66f62aa252d6 |
| Size | 2.4 KB |
| Checksum | sha256:306011553f9ff32f6120f8b8b0695b109e89175dbde36a6ee31f66f62aa252d6 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:01:58 (UTC) | 3 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:01:29 (UTC) | 3 | 2.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:42:02 (UTC) | 4 | 2.4 KB |