prod_reproduction/2022-lcWGS/run_lcWGS_call_L1.pbs

#!/usr/bin/env bash
#PBS -N lcWGS
#PBS -j oe
#PBS -l ncpus=8
#PBS -l nodes=1
#PBS -l mem=30G

sam_list=$sam_list

sams=(`cat $sam_list`)
echo "Samples:" ${sams[*]}
echo $lcwgs_path
echo "bash $lcwgs_path/run_lcWGS_call_L2.sh -r $SeqLen -i $indir  -d $out -s ${sams[${PBS_ARRAY_INDEX}]}"
sh $lcwgs_path/run_lcWGS_call_L2.sh -r $SeqLen -i $indir -x $lcwgs_path -d $out -s ${sams[${PBS_ARRAY_INDEX}]} &> $log.${sams[${PBS_ARRAY_INDEX}]}