parse config updates for fslmerge step

fslmerge/source/run

@@ -44,12 +44,28 @@ catTR_flag=$(jq -r <$MANIFEST '''.config.catTR.id')
 ###############################################################################
 # Parse config options from CONFIG file or MANIFEST
 
-if [[ -f $CONFIG_FILE ]]; then
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value)"' $CONFIG_FILE)
-else
-  CONFIG_FILE=$MANIFEST
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value.default)"' $CONFIG_FILE)
-fi
+function parse_config {
+
+  CONFIG_FILE=$FLYWHEEL_BASE/config.json
+  MANIFEST_FILE=$FLYWHEEL_BASE/manifest.json
+
+  if [[ -f $CONFIG_FILE ]]; then
+    echo -e "$(cat $CONFIG_FILE | jq -r '.config.'$1)"
+  else
+    CONFIG_FILE=$MANIFEST_FILE
+    echo -e "$(cat $MANIFEST_FILE | jq -r '.config.'$1'.default')"
+  fi
+
+}
+
+# String parsing
+config_catTime="$(parse_config 'catTime')"
+config_catX="$(parse_config 'catX')"
+config_catY="$(parse_config 'catY')"
+config_catZ="$(parse_config 'catZ')"
+config_auto="$(parse_config 'auto')"
+config_catTR="$(parse_config 'catTR')"
+config_base_outname="$(parse_config 'base_outname')"
 
 # Boolean parsing
 if [[ $config_catTime == 'true' ]]; then

manifest.json

@@ -9,9 +9,9 @@
   "source": "https://github.com/scitran-apps/afq-pipline",
   "license": "GPL-2.0",
   "flywheel": "0",
-  "version": "1.0.2",
+  "version": "1.0.3",
   "custom": {
-    "docker-image": "scitran/afq-pipeline:1.0.2"
+    "docker-image": "scitran/afq-pipeline:1.0.3"
   },
   "inputs": {
     "anatomical": {