From 0fe12185606e3b81ee1a6da7601b4d4c1fc945c8 Mon Sep 17 00:00:00 2001
From: boasvdp <boasvdp@gmail.com>
Date: Wed, 18 Sep 2024 11:28:56 +0200
Subject: [PATCH] fix: propagate user uploaded metadata

---
 run_pipeline.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/run_pipeline.sh b/run_pipeline.sh
index 355b0a0..ea7c910 100755
--- 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