Merge branch 'add_inferencedata_format' into 'master'

Adjusted pipeline to ensure config.yaml is written to results dir first.

See merge request !32

covid/ruffus_pipeline.py

@@ -57,21 +57,18 @@ def run_pipeline(global_config, results_directory, cli_options):
 
     # Pipeline starts here
     @rf.mkdir(results_directory)
+    @rf.originate(wd("config.yaml"), global_config)
+    def save_config(output_file, config):
+        with open(output_file, "w") as f:
+            yaml.dump(config, f)
+
+    @rf.follows(save_config)
     @rf.originate(wd("inferencedata.nc"), global_config)
     def process_data(output_file, config):
+
         _create_nc_file(output_file, pipeline_meta)
         assemble_data(output_file, config["ProcessData"])
 
-    @rf.transform(
-        process_data,
-        rf.formatter(),
-        wd("config.yaml"),
-        global_config,
-    )
-    def save_config(input_file, output_file, config):
-        with open(output_file, "w") as f:
-            yaml.dump(config, f)
-
     @rf.transform(
         process_data,
         rf.formatter(),