From ef68b7658b99c69e52f8a51736e0af03e2e969db Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Tue, 13 Jul 2021 11:58:31 +0200
Subject: [PATCH] validate config on required and optional fields #174
---
tests/input_files/config.yaml | 13 ++++++-----
workflow/Snakefile | 41 ++++++++++++++++++++++++++++++-----
2 files changed, 44 insertions(+), 10 deletions(-)
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
index f7a7410..f3cb261 100644
--- a/tests/input_files/config.yaml
+++ b/tests/input_files/config.yaml
@@ -1,4 +1,5 @@
---
+ # 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"
...
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 5f2434e..b5e295d 100644
--- a/workflow/Snakefile
+++ b/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,
--
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