nf-core/gatk4spark/baserecalibrator @ 0.0.0-0c7146d
Summary
Generate recalibration table for Base Quality Score Recalibration (BQSR)
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4SPARK_BASERECALIBRATOR } from 'nf-core/gatk4spark/baserecalibrator'
License
MIT License
Process
Name
|
GATK4SPARK_BASERECALIBRATOR |
|---|
Input
6 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM file from alignment *.{bam,cram}
|
input_index
file
|
BAI/CRAI file from alignment *.{bai,crai}
|
intervals
file
|
Bed file with the genomic regions included in the library (optional) |
fasta
file
|
The reference fasta file *.fasta
|
|---|
fai
file
|
Index of reference fasta file *.fasta.fai
|
|---|
dict
file
|
GATK sequence dictionary *.dict
|
|---|
known_sites
file
|
VCF files with known sites for indels / snps (optional) *.vcf.gz
|
|---|
known_sites_tbi
file
|
Tabix index of the known_sites (optional) *.vcf.gz.tbi
|
|---|
Output
2 channels
#1
table
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.table
file
|
Recalibration table from BaseRecalibrator *.{table}
|
#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 18:43:30 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4spark%2Fbaserecalibrator/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4spark/baserecalibrator/blobs/sha256:c11221ac7ed6a0a0cc1ed458b58486d4e4f24c9128cdff6d7e627020d0cb04be |
| Size | 3.8 KB |
| Checksum | sha256:c11221ac7ed6a0a0cc1ed458b58486d4e4f24c9128cdff6d7e627020d0cb04be |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:43:30 (UTC) | 1 | 3.8 KB | - |