Change ehdn outlier analysis script to handle qsub

ehdn/ehdn_getmultisampleprofile.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## ehdn_getmanifest.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
-## Usage :
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20200215
-## last revision date : 20200215
-## Known bugs : None
-
-EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
-REFERENCE="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
-WORKDIR="/work/gad/shared/analyse/STR/pipeline"
-
-cd "$WORKDIR"
-
-# Generate manifest and multisampleprofile by patient for all patients (to write file)
-for case in dijen*
-do
-    # Generate manifest for one patient with all samples (to write lines in the file)
-    for dijen in dijen*
-    do
-        if [ "x$dijen" = "x$case" ]
-        then
-	    echo -e "$dijen\tcase\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
-        else
-	    echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
-        fi
-    done > "$WORKDIR/$case/ehdn/$case.manifest.tsv"
-    # Generate multisampleprofile for one patient with all samples
-    "$EHDN" merge \
-	--reference "$REFERENCE" \
-	--manifest "$WORKDIR/$case/ehdn/$case.manifest.tsv" \
-	--output-prefix "$case/ehdn/$case"
-done
-
-

ehdn/ehdn_outlier.sh

-#! /bin/sh
-
-### ASDP PIPELINE ###
-## ehdn_getmanifest.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
-## Usage :
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20200215
-## last revision date : 20200215
-## Known bugs : None
-
-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"
-REFERENCE="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
-WORKDIR="/work/gad/shared/analyse/STR/pipeline"
-
-cd "$WORKDIR"
-
-# Generate manifest and multisampleprofile by patient for all patients (to write file)
-for case in dijen*
-do
-
-    # Generate manifest for one patient with all samples (to write lines in the file)
-    for dijen in dijen*
-    do
-	# Check if str_profile.json exists
-	if [ -f "$WORKDIR/$dijen/ehdn/$dijen.str_profile.json" ]
-        then
-	    if [ "x$dijen" = "x$case" ]
-            then
-		echo -e "$dijen\tcase\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
-            else
-		echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
-            fi
-	fi
-    done > "$WORKDIR/$case/ehdn/$case.manifest.tsv"
-
-    # Generate multisampleprofile for one patient with all samples
-    "$EHDN" merge \
-	--reference "$REFERENCE" \
-	--manifest "$WORKDIR/$case/ehdn/$case.manifest.tsv" \
-	--output-prefix "$case/ehdn/$case"
-
-    # Run locus-based comparison analysis
-    "$EHDN_OUTLIER" locus \
-	--manifest "$WORKDIR/$case/ehdn/$case.manifest.tsv" \
-	--multisample-profile "$WORKDIR/$case/ehdn/$case.multisample_profile.json" \
-	--output "$WORKDIR/$case/ehdn/$case.outlier_locus.tsv"
-
-    # Run motif_based comparison analysis
-    "$EHDN_OUTLIER" motif \
-        --manifest "$WORKDIR/$case/ehdn/$case.manifest.tsv" \
-        --multisample-profile "$WORKDIR/$case/ehdn/$case.multisample_profile.json" \
-        --output "$WORKDIR/$case/ehdn/$case.outlier_motif.tsv"
-done
-
-

wrapper_ehdn_outlier.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## Version: 0.0.1
+## Licence: FIXME
+## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
+## Usage: FIXME
+## Output: FIXME
+## Requirements: FIXME
+
+## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date: 20200215
+## Last revision date: 20200215
+## Known bugs: None
+
+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"
+REFERENCE="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
+WORKDIR="/work/gad/shared/analyse/STR/pipeline"
+
+# Log file path option
+if [ -z "$LOGFILE" ]
+then
+    LOGFILE=ehdn_outlier.$(date +"%F_%H-%M-%S").log
+fi
+
+# Logging
+exec 1>> "$LOGFILE" 2>&1
+echo "$(date +"%F_%H-%M-%S"): START"
+
+# Check if case is specified
+if [ -z "$CASE" ]
+then
+    echo "Dijen is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch ehdn_outlier.failed
+    exit 1
+fi
+
+# Generate manifest for one patient with all samples (to write lines in the file)
+cd "$WORKDIR"
+for dijen in dijen*
+do
+    # Check if str_profile.json exists
+    if [ -f "$WORKDIR/$dijen/ehdn/$dijen.str_profile.json" ]
+    then
+        if [ "x$dijen" = "x$CASE" ]
+        then
+        echo -e "$dijen\tcase\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
+        else
+        echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
+        fi
+    fi
+done > "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv"
+
+ehdn_outlier_exitcode=$?
+
+echo "ehdn_outlier exit code : $ehdn_outlier_exitcode"
+if [ $ehdn_outlier_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch ehdn_outlier.failed
+    exit 1
+fi
+
+# Generate multisampleprofile for one patient with all samples
+"$EHDN" merge \
+    --reference "$REFERENCE" \
+    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --output-prefix "$CASE/ehdn/$CASE"
+
+ehdn_outlier_exitcode=$?
+
+echo "ehdn_outlier exit code : $ehdn_outlier_exitcode"
+if [ $ehdn_outlier_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch ehdn_outlier.failed
+    exit 1
+fi
+
+# Run locus-based comparison analysis
+"$EHDN_OUTLIER" locus \
+    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --multisample-profile "$WORKDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
+    --output "$WORKDIR/$CASE/ehdn/$CASE.outlier_locus.tsv"
+
+ehdn_outlier_exitcode=$?
+
+echo "ehdn_outlier exit code : $ehdn_outlier_exitcode"
+if [ $ehdn_outlier_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch ehdn_outlier.failed
+    exit 1
+fi
+
+
+# Run motif_based comparison analysis
+"$EHDN_OUTLIER" motif \
+    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --multisample-profile "$WORKDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
+    --output "$WORKDIR/$CASE/ehdn/$CASE.outlier_motif.tsv"
+
+ehdn_outlier_exitcode=$?
+
+echo "ehdn_outlier exit code : $ehdn_outlier_exitcode"
+if [ $ehdn_outlier_exitcode != 0 ]
+then
+    echo "$(date +"%F_%H-%M-%S"): END"
+    touch ehdn_outlier.failed
+    exit 1
+fi
+
+echo "$(date +"%F_%H-%M-%S"): END"
+
+
+