Add README

.gitignore

@@ -5,5 +5,7 @@
 *.json
 *.sh.o*
 *.sh.po*
+*dijen*.o*
+*dijen*.po*
 *.failed
 #*#
\ No newline at end of file

README.md

+# STR detection pipeline
+
+ASDP PIPELINE
+Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+Version: 0.0.1
+Licence: FIXME
+Description: How to launch scripts to get STR genotype from genomes on all the locus tested
+
+1. Create genomes.list
+2. Specify output file in launch_pipeline.sh
+   Warning, don't overwrite existing files
+3. Launch launch_pipeline.sh
+   ```bash
+   nohup ./launch_pipeline.sh &
+   ```
+   Dependencies :
+   - genomes.list
+   - pipeline.sh
+   - launch_ehdn.sh
+   - launch_expansionhunter.sh
+   - launch_gangstr.sh
+   - launch_transfer.sh
+   - launch_tredparse.sh
+   - wrapper_delete.sh
+   - wrapper_ehdn.sh
+   - wrapper_expansionhunter.sh
+   - wrapper_gangstre.sh
+   - wrapper_transfer.sh
+   - wrapper_tredparse.sh
+4. Launch getResults.py
\ No newline at end of file

ehdn/ehdn_getmanifest.sh → ehdn/ehdn_getmultisampleprofile.sh

@@ -4,7 +4,7 @@
 ## ehdn_getmanifest.sh
 ## Version : 0.0.1
 ## Licence : FIXME
-## Description : script to generate automatically a manifest by patient in a tsv format
+## Description : script to generate automatically a manifest and multisampleprofile by patient in a tsv format
 ## Usage :
 ## Output : FIXME
 ## Requirements : FIXME
@@ -14,11 +14,13 @@
 ## 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 by patient for all patients (to write file)
+# 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)
@@ -31,6 +33,11 @@ do
 	    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