#!/bin/sh
#PBS -N FMBY2_prep
#PBS -j oe
#PBS -l ncpus=8
#PBS -l nodes=1
#PBS -l mem=10G

set -e
sams=(`cut -f1 $sam_list`)
panels=(`cut -f2 $sam_list`)
echo "script_dir:$script_dir"
echo "Samples:" ${sams[*]}
echo "panels:" ${panels[*]}

sh $script_dir/run_FMBY2_prep_L2.sh -i $fq_dir -o $out_dir -x $script_dir -c $cnv_dir -p ${panels[${PBS_ARRAY_INDEX}]} -s ${sams[${PBS_ARRAY_INDEX}]} &> $log.${sams[${PBS_ARRAY_INDEX}]}