Merge pull request #11 from RIVM-bioinformatics/test_metadata_propaga…

…tion fix: propagate user metadata
RIVM-bioinformatics · Sep 19, 2024 · bdf0db2 · bdf0db2
2 parents 8557edb + eabb78a
commit bdf0db2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -120,7 +120,7 @@ result=$?
 set +euo pipefail
 
 SEQ_KEYS=
-SEQ_ENV=`env | grep irods_input_sequencing`
+SEQ_ENV=`env | grep -E 'irods_input_(sequencing|user)'`
 for SEQ_AVU in ${SEQ_ENV}
 do
     SEQ_KEYS="${SEQ_KEYS} ${SEQ_AVU%%=*}"
@@ -132,7 +132,7 @@ 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