prod_reproduction/202307-IDTWES/run_WES_prep_L2.sh

#!/usr/bin/env bash
##Author: guochangquan
##Copyright 202206
##company: NuProbe

set -e

function usage() {
    echo "Usage: $0 [ -s <sample> ] [ -i <fq_dir> ] [ -o <analysis_dir> ] 
        [ -x <script_dir> ] [ -c <WES_CNV_outdir> ] [ -p <Pseudo_Panel> ]"
    echo "-s sample name"
    echo "-i input fastq dir"
    echo "-x script_dir"
    echo "-o analysis_dir"
    echo "-p Pseudo Panel[MBY2|MBY2_plus|FeBY2|FeBY2_plus|Jiayue|Xiangya]"
    echo "-c WES CNV outdir"
}

if [ $# -eq 0  ]
then
    usage
    exit
fi

while getopts ":s:c:x:o:i:p:h" opt; do
    case $opt in
        i)
            fq_dir=$OPTARG
            ;;
        o)
            out_dir=$OPTARG
            ;;
        p)
            panel=$OPTARG
            ;;
        s)
            sample=$OPTARG
            ;;
        c)
            cnv_dir=$OPTARG
            ;;
        x)
            script_dir=$OPTARG
            ;;
        h)
            usage
            exit
            ;;
        \?)
            echo "Invalid option: -$OPTARG" > /dev/stderr
            usage
            exit
            ;;
    esac
done
echo "Input FASTQ dir:" $fq_dir
echo "Output BAM dir:" $out_dir
echo "Sample Name:" $sample
echo "Sub-panel Type:" $panel
echo "CNV Analysis dir:" $cnv_dir
echo $script_dir

. $script_dir/conf/conf.cfg

#cd $out_dir/
test -d $out_dir/${sample} || mkdir ${out_dir}/${sample}
cd ${out_dir}/${sample}
### FASTQ TRIM and Mapping
test -s $sample.bam || sh $module/run_FQ2BAM_Speedseq.sh -s $sample -i $fq_dir -o $out_dir -x $script_dir

### SNV/INDEL CAll and annotation
test -s $sample.gatk.vcf.gz || sh $module/run_BAM2xlsx_SNV.sh -s $sample -o $out_dir -p $panel -x $script_dir -b $split_target
test -s $sample.sv.vcf.gz || sh $module/run_BAM2SV_Manta.sh -s $sample -o $out_dir/${sample} -x $script_dir
# sh $module/run_BAM2xlsx_SNV.sh -s $sample -o $out_dir -p $panel -x $script_dir -b $split_target
# sh $module/run_BAM2SV_Manta.sh -s $sample -o $out_dir/${sample} -x $script_dir

if [ $panel = "MBY2" -o $panel = "FeBY2" -o $panel = "FeBY2_plus" -o $panel = "MBY2_plus" ]
then
test -s $sample.vardict.vcf || sh $module/run_vardict_nt.sh -s $sample -o $out_dir -p $panel -x $script_dir
fi
### QC
test -s $sample.QC.xls || sh $module/run_QC.sh -s $sample -o $out_dir -x $script_dir
### yesuan
test -s yesuan/$sample.GT.xls || sh $module/run_yesuan.sh -s $sample -o $out_dir -p $panel -x $script_dir
### prepare for CNV
test -s $cnv_dir/$sample.pcov || sh $module/run_CNV_prep.sh -s $sample -o $out_dir -x $script_dir -c $cnv_dir
### roh
sh $module/run_ROH.sh -s $sample -o $out_dir -x $script_dir
### MT
sh $module/run_MT.sh -s $sample -o $out_dir -v $sample.gatk.vcf.gz -x $script_dir