Make EHDN pipeline more generic

TODO.org

@@ -2,6 +2,9 @@
 - [ ] Ecrire la doc
   - [ ] Ajouter dans la doc que Tred doit être ouvert dans virtual
   - [ ] Mode transfert
+  - [ ] Préciser qu'il ne faut rien ajouter manuellement dans les répertoires de OUTPUTDIR (car EHDN travaille sur tous les répertoires présents dans OUTPUTDIR, uniquement samples)
 - [ ] EHDN
   - [ ] Brancher EHDN et outlier
+  - [ ] Séparer case et contrôles
   - [ ] Ajouter EHDN dans GetResults
+- [ ] Ajouter le sample dans le nom de fichier de log

config.sh

@@ -33,6 +33,7 @@ GANGSTR_REGIONS="/work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed"
 EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
 EHDN_OUTLIER="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
 
+
 REF="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
 
 

launch_ehdn_outlier.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## Version: 0.0.1
-## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
-
-
-CASE="$1"
-DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunterDeNovoOutlier/$DATE"
-LOGFILE="$OUTPUTDIR/$DATE.$CASE.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"
-    CASE="$CASE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
-else 
-    mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q batch -N "ehdn_outlier_$CASE" -sync y -v CASE="$CASE",LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
-fi

launch_pipeline_ehdn_outlier.sh

@@ -6,12 +6,12 @@
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Description : script to launch the pipeline for STR detection with EHDN outlier
 
+# Source configuration file
+. "$(dirname "$0")/config.sh"
 
-LAUNCHER="$(readlink -f "$(dirname "$0")/launch_ehdn_outlier.sh")"
-
-cd "/work/gad/shared/analyse/STR/pipeline"
-printf "%s\n" dijen* |
-    /work/gad/shared/bin/parallel/parallel-20150522-1.el7.cern/bin/parallel \
-	--jobs 30 \
+cd "$OUTPUTDIR"
+printf "%s\n" * |
+    "$PARALLEL" \
+	--jobs "$PARALLEL_JOB_COUNT" \
         --line-buffer \
-        "$LAUNCHER"
+	"$(dirname "$0")/pipeline_ehdn_outlier.sh"

pipeline.sh

@@ -37,30 +37,30 @@ if [ "x$TRANSFER" = "xyes" ]
 then
     mkdir -p "$OUTPUTDIR"
     TRANSFER_JOB="transfer_$SAMPLE"
-    qsub -pe smp 1 -q "$TRANSFERQUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
+    qsub -pe smp 1 -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" "$(dirname "$0")/wrapper_transfer.sh"
     INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
 fi
 
 # Launch ExpansionHunter
 mkdir -p "$OUTPUTDIR/eh"
-qsub -pe smp 4 -q "$COMPUTEQUEUE"  -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
+qsub -pe smp 4 -q "$COMPUTE_QUEUE"  -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" "$(dirname "$0")/wrapper_expansionhunter.sh"
 
 # Launch Tredparse
 mkdir -p "$OUTPUTDIR/tredparse"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
+qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" "$(dirname "$0")/wrapper_tredparse.sh"
 
 # Launch GangSTR
 mkdir -p "$OUTPUTDIR/gangstr"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
+qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" "$(dirname "$0")/wrapper_gangstr.sh"
 
 # Launch ehdn profile
 mkdir -p "$OUTPUTDIR/ehdn"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn_profile.sh
+qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" "$(dirname "$0")/wrapper_ehdn_profile.sh"
 
 # Delete transfered bam and bai
 if [ "x$TRANSFER" = "xyes" ]
 then
-    qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
+    qsub -pe smp 1 -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" "$(dirname "$0")/wrapper_delete.sh"
 else
-    qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -b y echo "Nothing to delete."
+    qsub -pe smp 1 -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -b y echo "Nothing to delete."
 fi

pipeline_ehdn_outlier.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## Version: 0.0.1
+## Licence: AGPLv3
+## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
+
+# Source configuration file
+. "$(dirname "$0")/config.sh"
+
+CASE="$1"
+
+qsub -pe smp 1 -q "$COMPUTE_QUEUE" -N "ehdn_outlier_$CASE" -sync y -v CASE="$CASE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
+

wrapper_ehdn_outlier.sh

@@ -9,36 +9,31 @@
 # Source the configuration file
 . "$(dirname "$0")/config.sh"
 
-# Log file path option
-if [ -z "$LOGFILE" ]
-then
-    LOGFILE=ehdn_outlier.$(date +"%F_%H-%M-%S").log
-fi
-
 # Logging
+LOGFILE="$OUTPUTDIR/$CASE/ehdn/$CASE.ehdn_outlier.$(date +"%F_%H-%M-%S").log"
 exec 1>> "$LOGFILE" 2>&1
 echo "$(date +"%F_%H-%M-%S"): START"
 
 # Check if case is specified
 if [ -z "$CASE" ]
 then
-    echo "Dijen is not specified"
+    echo "Sample is not specified"
     echo "$(date +"%F_%H-%M-%S"): END"
     exit 1
 fi
 
 # Generate manifest for one patient with all samples (to write lines in the file)
 cd "$OUTPUTDIR"
-for dijen in dijen*
+for sample in *
 do
     # Check if str_profile.json exists
-    if [ -f "$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json" ]
+    if [ -f "$OUTPUTDIR/$sample/ehdn/$sample.str_profile.json" ]
     then
-        if [ "x$dijen" = "x$CASE" ]
+        if [ "x$sample" = "x$CASE" ]
         then
-        echo -e "$dijen\tcase\t$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json"
+        echo -e "$sample\tcase\t$OUTPUTDIR/$sample/ehdn/$sample.str_profile.json"
         else
-        echo -e "$dijen\tcontrol\t$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json"
+        echo -e "$sample\tcontrol\t$OUTPUTDIR/$sample/ehdn/$sample.str_profile.json"
         fi
     fi
 done > "$OUTPUTDIR/$CASE/ehdn/$CASE.manifest.tsv"