nf-core/gatk4/asereadcounter @ 0.0.0-0c7146d
Summary
Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_ASEREADCOUNTER } from 'nf-core/gatk4/asereadcounter'
License
MIT License
Process
Name
|
GATK4_ASEREADCOUNTER |
|---|
Input
5 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file *.{bam}
|
bai
file
|
index file for BAM file *.{bai}
|
vcf
file
|
VCF file *.{vcf.gz}
|
tbi
file
|
index file for VCF file *.{vcf.gz.tbi}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. |
|---|---|
fasta
file
|
fasta file *.{fasta,fa}
|
#3
tuple
meta3
map
|
Groovy Map containing reference information e.g. |
|---|---|
fai
file
|
fasta index file *.{fai}
|
#4
tuple
meta4
map
|
Groovy Map containing reference information e.g. |
|---|---|
dict
file
|
dictionary file *.{dict}
|
intervals
file
|
interval file |
|---|
Output
2 channels
#1
csv
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|
#2
versions_gatk4
tuple
${task.process}
string
|
The name of the process |
|---|---|
gatk4
string
|
The name of the tool |
gatk --version | sed -n '/GATK.*v/s/.*v//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gatk4 | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. | https://gatk.broadinstitute.org/hc/en-us |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:41:02 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fasereadcounter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/asereadcounter/blobs/sha256:a393eabc05b28778f31f1ce7c1e77dd099c6f9a2313db9a802ee22c7f83309c5 |
| Size | 3.0 KB |
| Checksum | sha256:a393eabc05b28778f31f1ce7c1e77dd099c6f9a2313db9a802ee22c7f83309c5 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:02 (UTC) | 1 | 3.0 KB | - |