Create wrapper for STRetch

wrapper_stretch.sh

 #! /bin/sh
 
 ### ASDP PIPELINE ###
-## wrapper_gangstr.sh
+## wrapper_stretch.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
+## Description : a wrapper for qsubing STRetch 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_stretch.sh
 ## Output : FIXME
 ## Requirements : FIXME
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191104
-## last revision date : 20191104
+## Creation Date : 20191118
+## last revision date : 20191118
 ## Known bugs : None
 
 
 # Log file path option
 if [ -z "$LOGFILE" ]
 then
-    LOGFILE=gangstr.$(date +"%F_%H-%M-%S").log
+    LOGFILE=stretch.$(date +"%F_%H-%M-%S").log
 fi
 
 # Logging
@@ -31,7 +31,7 @@ if [ ! -f "$INPUTFILE" ]
 then
     echo "Input file '$INPUTFILE' does not exist"
     echo "$(date +"%F_%H-%M-%S"): END"
-    touch gangstr.failed
+    touch stretch.failed
     exit 1
 fi
 
@@ -40,32 +40,32 @@ if [ -z "$OUTPUTPREFIX" ]
 then
     echo "Output prefix is not specified"
     echo "$(date +"%F_%H-%M-%S"): END"
-    touch gangstr.failed
+    touch stretch.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"
+echo "cd "$OUTPUTDIR"
+/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
+    run -p \
+    input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
+    /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
+    "$INPUTFILE""
 
-/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
+cd "$OUTPUTDIR"
+/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
+    run -p
+    input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
+    /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
+    "$INPUTFILE"
 
-gangstr_exitcode=$?
+stretch_exitcode=$?
 
-echo "gangstr exit code : $gangstr_exitcode"
-if [ $gangstr_exitcode != 0 ]
+echo "stretch exit code : $stretch_exitcode"
+if [ $stretch_exitcode != 0 ]
 then
     echo "$(date +"%F_%H-%M-%S"): END"
-    touch gangstr.failed
+    touch stretch.failed
     exit 1
 fi