From 1d3ace6ec5dc7639479f20f33e067f0730becf2d Mon Sep 17 00:00:00 2001
From: Dominik Burri <dominik.burri@unibas.ch>
Date: Thu, 15 Jul 2021 13:40:02 +0000
Subject: [PATCH] Validation of configuration file with a json schema
`resources/config_schema.json` using the snakemake utility **validate**. The
schema includes all the fields from `tests/input_files/config.yaml`, assigns
certain fields as required and forbids the use of additional fields. All of
the optional fields include default values, taken from the config above,
except `rule_config` which has no default.
Added author name and author email as optional fields in `tests/input_files/config.yaml`, and added it into the multiqc report.
---
resources/config_schema.json | 66 +++++++++++++++++++++
tests/input_files/config.mutliple_lanes.yml | 2 +-
tests/input_files/config.yaml | 6 +-
tests/input_files/config_alfa.yaml | 13 ++--
workflow/Snakefile | 29 ++++++---
5 files changed, 99 insertions(+), 17 deletions(-)
create mode 100644 resources/config_schema.json
diff --git a/resources/config_schema.json b/resources/config_schema.json
new file mode 100644
index 0000000..1ad7846
--- /dev/null
+++ b/resources/config_schema.json
@@ -0,0 +1,66 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema#",
+ "title": "Configuration schema",
+ "required": ["samples", "output_dir", "log_dir", "kallisto_indexes", "salmon_indexes", "star_indexes", "alfa_indexes"],
+ "type": "object",
+ "additionalProperties": false,
+ "properties": {
+ "samples": {
+ "type": "string",
+ "description": "Path to samples table."
+ },
+ "output_dir": {
+ "type": "string",
+ "description": "Path to output directory."
+ },
+ "log_dir": {
+ "type": "string",
+ "description": "Path to log directory."
+ },
+ "kallisto_indexes": {
+ "type": "string",
+ "description": "Path to kallisto indexes directory."
+ },
+ "salmon_indexes": {
+ "type": "string",
+ "description": "Path to salmon indexes directory."
+ },
+ "star_indexes": {
+ "type": "string",
+ "description": "Path to star indexes directory."
+ },
+ "alfa_indexes": {
+ "type": "string",
+ "description": "Path to alfa indexes directory."
+ },
+ "rule_config": {
+ "type": "string",
+ "description": "Path to rule configuration file."
+ },
+ "report_description": {
+ "type": "string",
+ "description": "Description of the run to appear in the multiqc report.",
+ "default": "No description provided by user."
+ },
+ "report_logo": {
+ "type": "string",
+ "description": "Relative path to image to display as logo in multiqc report.",
+ "default": "../../images/logo.128px.png"
+ },
+ "report_url": {
+ "type": "string",
+ "description": "URL to appear in multiqc report.",
+ "default": "https://zavolan.biozentrum.unibas.ch/"
+ },
+ "author_name": {
+ "type": "string",
+ "description": "Full author name to display in multiqc report.",
+ "default": "NA"
+ },
+ "author_email": {
+ "type": "string",
+ "description": "Author e-mail address to display in multiqc report.",
+ "default": "NA"
+ }
+ }
+}
diff --git a/tests/input_files/config.mutliple_lanes.yml b/tests/input_files/config.mutliple_lanes.yml
index 3d04a01..8fb3406 100644
--- a/tests/input_files/config.mutliple_lanes.yml
+++ b/tests/input_files/config.mutliple_lanes.yml
@@ -1,12 +1,12 @@
---
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"
+ 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/"
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
index 853a8a7..1fc480c 100644
--- a/tests/input_files/config.yaml
+++ b/tests/input_files/config.yaml
@@ -1,13 +1,17 @@
---
+ # 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"
salmon_indexes: "results/salmon_indexes"
star_indexes: "results/star_indexes"
alfa_indexes: "results/alfa_indexes"
+ # Optional fields
+ 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/"
+ author_name: "NA"
+ author_email: "NA"
...
diff --git a/tests/input_files/config_alfa.yaml b/tests/input_files/config_alfa.yaml
index cdcfb8b..5edcd7e 100644
--- a/tests/input_files/config_alfa.yaml
+++ b/tests/input_files/config_alfa.yaml
@@ -1,11 +1,12 @@
---
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/"
+ 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"
+ 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/"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index d46c511..fc268e4 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -5,6 +5,7 @@ import shutil
import yaml
from shlex import quote
from typing import Tuple
+from snakemake.utils import validate
## Preparations
# Get sample table
@@ -17,16 +18,22 @@ samples_table = pd.read_csv(
sep="\t",
)
+# Validat config
+validate(config, os.path.join("..", "resources", "config_schema.json"))
+logger.info(f'Config file after validation: {config}')
+
# Parse YAML rule config file
-if 'rule_config' in config and config['rule_config']:
- try:
- with open(config['rule_config']) as _file:
- rule_config = yaml.safe_load(_file)
- logger.info(f"Loaded rule_config from {config['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! ")
- raise
-else:
+try:
+ with open(config['rule_config']) as _file:
+ rule_config = yaml.safe_load(_file)
+ logger.info(f"Loaded rule_config from {config['rule_config']}.")
+except TypeError:
+ logger.error(f'No string supplied at field "rule_config", but: {type(config["rule_config"])} with content: {config["rule_config"]}')
+ raise
+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! ")
+ raise
+except KeyError:
rule_config = {}
logger.warning(f"No rule config specified: using default values for all tools.")
@@ -1547,6 +1554,8 @@ rule prepare_multiqc_config:
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'],
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
@@ -1572,6 +1581,8 @@ rule prepare_multiqc_config:
--intro-text '{params.multiqc_intro_text}' \
--custom-logo {params.logo_path} \
--url '{params.url}' \
+ --author-name {params.author_name} \
+ --author-email {params.author_email} \
{params.additional_params}) \
1> {log.stdout} 2> {log.stderr}"
--
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