#!/bin/sh
SIZE=1
if [ "$#" -eq 1 ]; then
  SIZE=$1
fi

cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
cp *.fastq.gz /workspace/launch/.
time nextflow run -c nextflow-k8s.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc