#!/bin/bash

if [ "$#" -ne 2 ]; then
  echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
  exit
fi
SIZE=$1
LOGOUT=$2

TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz

MYDIR=$(pwd)

mkdir -p /workspace/sarek
mkdir -p /workspace/launch/work
cp nextflow-k8s.config /workspace/sarek/nextflow-k8s.config
cp runtimes.csv /workspace/launch/work/runtimes.csv
cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv

cd /workspace/launch
tar xzf ${TESTDATA_ARCHIVE}

cd /workspace/sarek
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
rm -rf out
cp .nextflow.log /${LOGOUT}

cd ${MYDIR}
rm -rf /workspace/*