This repo replaces the script previously located at /scratch/work/cgsb/scripts/variant_calling/gatk4
After building your nextflow.config file and loading the nextflow module (ex: module load nextflow/20.11.0-edge), use the following command to call the script directly from this repo, where the -r parameter specifies the version of the script you would like to run.
nextflow run gencorefacility/hpc-gatk4 -c nextflow.config -r v1.1
v1.0 is the original version of the script which was previously located at /scratch/work/cgsb/scripts/variant_calling/gatk4. Use this version to reproduce a previous analysis or analyze new data using the same pipeline.
v1.1 is an updated version of the script which uses an updated version of GATK4 (4.2.4.1).