validate config on required and optional fields #174

tests/input_files/config.yaml

 ---
+  # Required fields
   samples: "../input_files/samples.tsv"
   rule_config: "../input_files/rule_config.yaml"
   output_dir: "results"
@@ -7,9 +8,11 @@
   salmon_indexes: "results/salmon_indexes"
   star_indexes: "results/star_indexes"
   alfa_indexes: "results/alfa_indexes"
-  report_description: "No description provided by user"
-  report_logo: "../../images/logo.128px.png"
-  report_url: "https://zavolan.biozentrum.unibas.ch/"
-  author_name: "NA"
-  author_email: "NA"
+  # Optional fields
+  optional:
+    report_description: "No description provided by user"
+    report_logo: "../../images/logo.128px.png"
+    report_url: "https://zavolan.biozentrum.unibas.ch/"
+    author_name: "NA"
+    author_email: "NA"
 ...

workflow/Snakefile

@@ -17,6 +17,37 @@ samples_table = pd.read_csv(
     sep="\t",
 )
 
+# Validate config with template config
+template_config_path = os.path.join(
+            workflow.current_basedir, 
+            '..',
+            'tests', 
+            'input_files', 
+            'config.yaml')
+try:
+    with open(template_config_path) as _file:
+        template_config = yaml.safe_load(_file)
+    logger.info(f"Loaded template config from {template_config_path}.")
+    # Check if config contains required fields in example config
+    for key in template_config:
+        if key != 'optional':
+            assert key in config
+except FileNotFoundError:
+    logger.error(f"No config file found at {template_config_path}! ")
+    raise
+except AssertionError:
+    logger.error(f"Required config fields from {template_config_path} do not match {config.keys()}")
+    raise
+# Check if optional field available
+if 'optional' not in config:
+    config['optional'] = {}
+# Check optional fields and include in config if not present
+for optkey, value in template_config['optional'].items():
+    if optkey not in config['optional']:
+        config['optional'][optkey] = value
+        logger.info(f"Added optional field: \"{optkey}\" with value: \"{value}\" to config.")
+
+
 # Parse YAML rule config file
 if 'rule_config' in config and config['rule_config']:
     try:
@@ -1544,11 +1575,11 @@ rule prepare_multiqc_config:
             "multiqc_config.yaml")
 
     params:
-        logo_path = config['report_logo'],
-        multiqc_intro_text = config['report_description'],
-        url = config['report_url'],
-        author_name = config['author_name'],
-        author_email = config['author_email'],
+        logo_path = config['optional']['report_logo'],
+        multiqc_intro_text = config['optional']['report_description'],
+        url = config['optional']['report_url'],
+        author_name = config['optional']['author_name'],
+        author_email = config['optional']['author_email'],
         additional_params = parse_rule_config(
             rule_config,
             current_rule=current_rule,