#!/bin/bash

export NXF_DEFAULT_DSL=1

while read g; do
  echo "Run StellarPGx for all samples and gene: ${g^^}"
  nextflow run main.nf -profile standard --build hg38 --gene $g
  echo 'done. Parsing results...'
  for f in results/$g/alleles/* ; do python3 stellar_parser.py $f; done
done < genes.txt

#rm -r results/*