prod_reproduction/2022-lcWGS/run_lcWGS_copy_L1.pbs

#!/usr/bin/env bash
#PBS -N lcWGS_copy
#PBS -j oe
#PBS -l ncpus=8
#PBS -l nodes=1
#PBS -l mem=10G

sam_list=$sam_list

sams=(`cat $sam_list`)
echo "Samples:" ${sams[*]}
echo $lcwgs_path
test -d $out/QC || mkdir $out/QC
test -d $res_dir/lcWGS || mkdir -p $res_dir/lcWGS
for sample in ${sams[*]}
do
    cp $out/$sample/${sample}.lcWGS.QC.xls $out/QC
    cp $out/$sample/${sample}.lcWGS.QC.xls $res_dir/lcWGS
    cp $out/$sample/${sample}.CNV.xls $res_dir/lcWGS
    cp $out/$sample/${sample}_?_w100.png $res_dir/lcWGS
    cp $out/$sample/${sample}_QC_plot.pdf $res_dir/lcWGS
    cp $out/$sample/${sample}_segment_call.pdf $res_dir/lcWGS
    cp $out/$sample/${sample}.chr_CR.xls $res_dir/lcWGS
    cp $out/$sample/${sample}_?_dnacopy.out.tsv $res_dir/lcWGS
    cp $lcwgs_path/report/lcWGS.v2023.report.CNV.xlsx $res_dir/lcWGS/${sample}.report.CNV.xlsx

done

chmod g-w $res_dir/lcWGS
cd $out/QC
cat *.lcWGS.QC.xls |sort |uniq |grep '^Sample\s' > head.lcWGS.QC.xls
cat *.lcWGS.QC.xls |sort |uniq |grep -v '^Sample\s'|cat head.lcWGS.QC.xls -  > $batch.lcWGS_QC.xls && rm *.lcWGS.QC.xls