Update queue and add stretch wrapper

launch_expansionhunter.sh

@@ -11,10 +11,10 @@
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Creation Date : 20191102
-## last revision date : 20191102
+## last revision date : 20191126
 ## Known bugs : None
 
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
@@ -27,5 +27,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
+    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
 fi

launch_gangstr.sh

@@ -11,21 +11,23 @@
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Creation Date : 20191104
-## last revision date : 20191117
+## last revision date : 20191126
 ## Known bugs : None
 
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
 LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
+INSERTMEAN="359.4"
+INSERTDEV="80.1204"
 
 # Launch the script on local host with --local option and on SGE with qsub without the --local option
 if [ $# -eq 1 ] && [ "x$1" = x--local ]
 then
     mkdir -p "$OUTPUTDIR"
-    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh"
+    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" INSERTMEAN="$INSERTMEAN" INSERTDEV="$INSERTDEV" "$(dirname "$0")/wrapper_gangstr.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh
+    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE",INSERTMEAN="$INSERTMEAN",INSERTDEV="$INSERTDEV" wrapper_gangstr.sh
 fi

launch_lobstr.sh

@@ -14,7 +14,7 @@
 ## last revision date : 20191104
 ## Known bugs : None
 
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18/dijen017.sorted.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"

launch_stretch.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## launch_wrapper_stretch.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to launch the wrapper for qsubing STRetch script for STR detection
+## Usage : FIXME
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191118
+## last revision date : 20191127
+## Known bugs : None
+
+# INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
+
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/shortdijen017/dijen017.short.bam
+DATE="$(date +"%F_%H-%M-%S")"
+OUTPUTDIR="/work/gad/shared/analyse/STR/STRetch/$DATE"
+LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
+
+# Launch the script on local host with --local option and on SGE with qsub without the --local option
+if [ $# -eq 1 ] && [ "x$1" = x--local ]
+then
+    mkdir -p "$OUTPUTDIR"
+    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_stretch.sh"
+else 
+    mkdir -p "$OUTPUTDIR"
+    qsub -pe smp 16 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_stretch.sh
+fi

launch_tredparse.sh

@@ -11,10 +11,10 @@
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Creation Date : 20191103
-## last revision date : 20191103
+## last revision date : 20191126
 ## Known bugs : None
 
-INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE"
 LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"

wrapper_gangstr.sh

@@ -11,7 +11,7 @@
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Creation Date : 20191104
-## last revision date : 20191104
+## last revision date : 20191127
 ## Known bugs : None
 
 
@@ -50,14 +50,19 @@ echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
     --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
     --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
     --out "$OUTPUTPREFIX" \
-    --verbose"
+    --verbose \
+    --insertmean "$INSERTMEAN" \
+    --insertsdev "$INSERTDEV""
 
 /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
+    --verbose \
+    --insertmean "$INSERTMEAN" \
+    --insertsdev "$INSERTDEV"
+
 
 gangstr_exitcode=$?
 

wrapper_samtoolssortbyread.sh

 #! /bin/sh
 
-samtools sort -n -@64 -T /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18  -o /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam
+samtools sort -n -@64 --check=quiet -T sortbyread  /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26  -o /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam

wrapper_stretch.sh

@@ -47,15 +47,13 @@ fi
 # Launch script command and check exit code
 echo "cd "$OUTPUTDIR"
 /work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
-    run -p \
-    input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
+    run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
     /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
     "$INPUTFILE""
 
 cd "$OUTPUTDIR"
 /work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
-    run -p
-    input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
+    run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
     /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
     "$INPUTFILE"