Add script to generate manifest by patient for EHDN

ehdn/ehdn_getmanifest.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## ehdn_getmanifest.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to generate automatically a manifest 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
+
+WORKDIR="/work/gad/shared/analyse/STR/pipeline"
+
+cd "$WORKDIR"
+
+# Generate manifest by patient for all patients (to write file)
+for case in dijen*
+do
+    # Generate manifest for one patient with all samples (to write lines in the file)
+    for dijen in dijen*
+    do
+        if [ "x$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"
+done
+
+