adjust all config files and test cases to new optional field.

scripts/prepare_inputs.py

@@ -678,9 +678,10 @@ def main(args):
   salmon_indexes: "{salmon_indexes}"
   star_indexes: "{star_indexes}"
   alfa_indexes: "{alfa_indexes}"
-  report_description: "{args.description}"
-  report_logo: "{args.logo}"
-  report_url: "{args.url}"
+  optional:
+    report_description: "{args.description}"
+    report_logo: "{args.logo}"
+    report_url: "{args.url}"
 ...
 '''
     args.config_file.write(config_file_content)

tests/input_files/config.mutliple_lanes.yml

 ---
   samples: "../input_files/samples.multiple_lanes.tsv"
-  rule_config: "../input_files/rule_config.yaml"
   output_dir: "results"
   log_dir: "logs"
   kallisto_indexes: "results/kallisto_indexes"
   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:
+    rule_config: "../input_files/rule_config.yaml"
+    report_description: "No description provided by user"
+    report_logo: "../../images/logo.128px.png"
+    report_url: "https://zavolan.biozentrum.unibas.ch/"
 ...

tests/input_files/config.yaml

 ---
   # Required fields
   samples: "../input_files/samples.tsv"
-  rule_config: "../input_files/rule_config.yaml"
   output_dir: "results"
   log_dir: "logs"
   kallisto_indexes: "results/kallisto_indexes"
@@ -10,6 +9,7 @@
   alfa_indexes: "results/alfa_indexes"
   # Optional fields
   optional:
+    rule_config: "../input_files/rule_config.yaml"
     report_description: "No description provided by user"
     report_logo: "../../images/logo.128px.png"
     report_url: "https://zavolan.biozentrum.unibas.ch/"

tests/input_files/config_alfa.yaml

 ---
   samples: "../input_files/samples_alfa.tsv"
-  output_dir: "results/"
-  log_dir: "logs/"
-  kallisto_indexes: "results/kallisto_indexes/"
-  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"
+  output_dir: "results"
+  log_dir: "logs"
+  kallisto_indexes: "results/kallisto_indexes"
+  salmon_indexes: "results/salmon_indexes"
+  star_indexes: "results/star_indexes"
+  alfa_indexes: "results/alfa_indexes"
+  optional:
+    rule_config: "../input_files/rule_config.yaml"
+    report_description: "No description provided by user"
+    report_logo: "../../images/logo.128px.png"
+    report_url: "https://zavolan.biozentrum.unibas.ch/"
 ...

tests/test_scripts_prepare_inputs_table/expected_output.md5

-40bd0f0fcecdd0d9bc932f63c2811478  config.yaml
+90e90bb60335a2e17cd40cbf058af7b7  config.yaml
 c8dcc5a203e9046806c4090525960151  samples.tsv

workflow/Snakefile

@@ -49,13 +49,13 @@ for optkey, value in template_config['optional'].items():
 
 
 # Parse YAML rule config file
-if 'rule_config' in config and config['rule_config']:
+if 'rule_config' in config['optional'] and config['optional']['rule_config']:
     try:
-        with open(config['rule_config']) as _file:
+        with open(config['optional']['rule_config']) as _file:
             rule_config = yaml.safe_load(_file)
-        logger.info(f"Loaded rule_config from {config['rule_config']}.")
+        logger.info(f"Loaded rule_config from {config['optional']['rule_config']}.")
     except FileNotFoundError:
-        logger.error(f"No rule config file found at {config['rule_config']}. Either provide file or remove rule_config parameter from config.yaml! ")
+        logger.error(f"No rule config file found at {config['optional']['rule_config']}. Either provide file or remove rule_config parameter from config.yaml! ")
         raise
 else:
     rule_config = {}