This is a GATK based variant calling workflow written in Nextflow.
The workflow is contained in the main.nf script.
The workflow has the following inputs:
- reference genome, indexed with bwa index: the path to the FASTA file (local or S3) can be given in the "--ref" commandline option
- sample sheet CSV file with header "sample,fastq_1,fastq_2"
Example sample sheets are included.
To run the workflow, please modify run-ec2-test.sh or run-local-test.sh with paths to your data