linting

workflow/Snakefile

@@ -24,11 +24,7 @@ include: "rules/11-prep_for_phyloseq.smk"
 include: "rules/12-phyloseq_abund_blast.smk"
 include: "rules/13-ampvis2_std_plots.smk"
 include: "rules/capture_config.smk" # <- this is a custom rule to capture the config file and changes to config file
-### Validate configuration options for "include_sintax_output" and "include_blast_output"
-def validate_boolean_config(config_value, config_name):
-    if not isinstance(config_value, bool):
-        raise ValueError(f"Invalid value for {config_name}: '{config_value}'. It must be True or False (case-sensitive).")
-# Validate the configuration values
+# Validate the configuration values, using 
 validate_boolean_config(config["include_blast_output"], "include_blast_output")
 validate_boolean_config(config["include_sintax_output"], "include_sintax_output")
 

workflow/rules/common.smk

@@ -1,7 +1,10 @@
 ## Wildcards helper function - new version, this is the one located in the exp branch.
 import glob
 import os
-
+### Validate configuration options for "include_sintax_output" and "include_blast_output"
+def validate_boolean_config(config_value, config_name):
+    if not isinstance(config_value, bool):
+        raise ValueError(f"Invalid value for {config_name}: '{config_value}'. It must be True or False (case-sensitive).")
 # Wildcards helper function
 def listFastq(wildcards):
     sample_path = os.path.join(config['input_dir'])

workflow/scripts/nanoplot.sh

@@ -158,7 +158,6 @@ statistics() {
 export -f statistics
 
 parallel -j "$JobNr" statistics ::: "${files[@]}" ::: $((threads / JobNr)) ::: "$output_dir" 
-module purge
 
 
 echo "Check your amplicon size and quality before setting parameters for chopper filtering, used in the snakemake workflow. Filtering settings can be changed in the config file. \"config/config.yaml\""