Load selected config file configuration in run-pipeline script instea…

…d of in fetch_data script
Sage-Bionetworks · May 1, 2024 · dc90f8c · dc90f8c
1 parent d932f33
commit dc90f8c
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diff --git a/pipeline/run-pipeline.R b/pipeline/run-pipeline.R
@@ -1,3 +1,10 @@
+# Get config variables
+config::get(
+  file = "config/config.yml", 
+  config = "staging"
+) %>% 
+  list2env(envir = .GlobalEnv)
+
 # Fetch data
 tictoc::tic(msg = "INFO: Fetch data")
 source("scripts/fetch-data/fetch_data.R")

diff --git a/scripts/fetch-data/fetch_data.R b/scripts/fetch-data/fetch_data.R
@@ -4,13 +4,6 @@ library(dplyr)
 
 cat("Fetching data\n")
 
-# Get config variables
-config::get(
-  file = "config/config.yml", 
-  config = "prod"
-) %>% 
-  list2env(envir = .GlobalEnv)
-
 synLogin()
 
 # Get input files from synapse