Create wrapper_gangstr.sh

wrapper_gangstr.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## wrapper_gangstr.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : a wrapper for qsubing GangSTR script for STR detection
+## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_gangstr.sh
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191104
+## last revision date : 20191104
+## Known bugs : None
+
+
+# Log file path option
+if [ -z "$LOGFILE" ]
+then
+    LOGFILE=gangstr.$(date +"%F_%H-%M-%S").log
+fi
+
+# Logging
+exec 1>> "$LOGFILE" 2>&1
+echo "$(date +"%F_%H-%M-%S"): START"
+
+
+# Check if input file exists
+if [ ! -f "$INPUTFILE" ]
+then
+    echo "Input file '$INPUTFILE' does not exist"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch gangstr.failed
+    exit 1
+fi
+
+# Check if output prefix is specified
+if [ -z "$OUTPUTPREFIX" ]
+then
+    echo "Output prefix is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch gangstr.failed
+    exit 1
+fi
+
+# Launch script command and check exit code
+echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
+    --bam "$INPUTFILE" \
+    --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
+    --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
+    --out "$OUTPUTPREFIX" \
+    --verbose"
+
+/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
+    --bam "$INPUTFILE" \
+    --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
+    --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
+    --out "$OUTPUTPREFIX" \
+    --verbose
+
+gangstr_exitcode=$?
+
+echo "gangstr exit code : $gangstr_exitcode"
+if [ $gangstr_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch gangstr.failed
+    exit 1
+fi
+
+echo "$(date +"%F_%H-%M-%S"): END"