Do EHDN outlier analyses (not parallelized)

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
+
+