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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:02:34 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fasereadcounter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/asereadcounter/blobs/sha256:01e935f8211a92331e54c7a34ce420a0bece2e7c13d08a4f16cf21a1c7c9e207 |
| Size | 3.0 KB |
| Checksum | sha256:01e935f8211a92331e54c7a34ce420a0bece2e7c13d08a4f16cf21a1c7c9e207 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:18:23 (UTC) | 4 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:02:34 (UTC) | 3 | 3.0 KB |