From 1e5e058dc91f1d2dbe1da88e5f5f266fe3eec771 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Tue, 13 Jul 2021 14:31:43 +0200
Subject: [PATCH] adjust all config files and test cases to new optional field.
---
scripts/prepare_inputs.py | 7 +++---
tests/input_files/config.mutliple_lanes.yml | 11 +++++-----
tests/input_files/config.yaml | 2 +-
tests/input_files/config_alfa.yaml | 22 +++++++++----------
.../expected_output.md5 | 2 +-
workflow/Snakefile | 8 +++----
6 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/scripts/prepare_inputs.py b/scripts/prepare_inputs.py
index 426902a..e47fa3d 100755
--- a/scripts/prepare_inputs.py
+++ b/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)
diff --git a/tests/input_files/config.mutliple_lanes.yml b/tests/input_files/config.mutliple_lanes.yml
index ada2c6b..016692d 100644
--- a/tests/input_files/config.mutliple_lanes.yml
+++ b/tests/input_files/config.mutliple_lanes.yml
@@ -1,15 +1,14 @@
---
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/"
...
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
index f3cb261..54edf9c 100644
--- a/tests/input_files/config.yaml
+++ b/tests/input_files/config.yaml
@@ -1,7 +1,6 @@
---
# 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/"
diff --git a/tests/input_files/config_alfa.yaml b/tests/input_files/config_alfa.yaml
index 60c1e0a..06decc6 100644
--- a/tests/input_files/config_alfa.yaml
+++ b/tests/input_files/config_alfa.yaml
@@ -1,14 +1,14 @@
---
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/"
...
diff --git a/tests/test_scripts_prepare_inputs_table/expected_output.md5 b/tests/test_scripts_prepare_inputs_table/expected_output.md5
index 53afed5..dc555cc 100644
--- a/tests/test_scripts_prepare_inputs_table/expected_output.md5
+++ b/tests/test_scripts_prepare_inputs_table/expected_output.md5
@@ -1,2 +1,2 @@
-40bd0f0fcecdd0d9bc932f63c2811478 config.yaml
+90e90bb60335a2e17cd40cbf058af7b7 config.yaml
c8dcc5a203e9046806c4090525960151 samples.tsv
diff --git a/workflow/Snakefile b/workflow/Snakefile
index b5e295d..e5d270b 100644
--- a/workflow/Snakefile
+++ b/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 = {}
--
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