fix: propagate user uploaded metadata

RIVM-bioinformatics · Sep 18, 2024 · 0fe1218 · 0fe1218
1 parent 5013368
commit 0fe1218
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -129,12 +129,13 @@ do
 done
 
 for key in $SEQ_KEYS irods_input_illumina__Flowcell irods_input_illumina__Instrument \
-    irods_input_illumina__Date irods_input_illumina__Run_number irods_input_illumina__Run_Id
+    irods_input_illumina__Date irods_input_illumina__Run_number irods_input_illumina__Run_Id \
+    irods_input__user__include_in_surveillance irods_input__user__validation_set
 do
     if [ ! -z ${!key} ] ; then
         attrname=${key:12}
         attrname=${attrname/__/::}
-        echo "${attrname}: '${!key}'" >> ${OUTPUTDIR}/metadata.yml
+        echo "${attrname}: '${!key}'" >> ${output_dir}/metadata.yml
     fi
 done