Add case-sensitive validation for config change through command line

workflow/Snakefile

@@ -8,7 +8,7 @@ from snakemake.utils import min_version
 min_version("7.18.2")
 
 configfile: "config/config.yaml"
-
+# Rules
 include: "rules/common.smk"
 include: "rules/01-concatenate_fastq.smk"
 include: "rules/02-filtering.smk"
@@ -19,11 +19,22 @@ include: "rules/06-relabel.smk"
 include: "rules/07-clustering_identity.smk"
 include: "rules/08-taxonomy.smk"
 include: "rules/09-fix_otu_table.smk"
-include: "rules/10-prep_for_ampvis2.smk" # <- shouldn't be necessary, amp_load() reads sintax files directly, see "taxonomy" here https://kasperskytte.github.io/ampvis2/reference/amp_load.html#arguments-1
+include: "rules/10-prep_for_ampvis2.smk"
 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_boolean_config(config["include_blast_output"], "include_blast_output")
+validate_boolean_config(config["include_sintax_output"], "include_sintax_output")
+
+# Assign the configuration values to variables
+include_blast_output = config["include_blast_output"]
+include_sintax_output = config["include_sintax_output"]
 ## Function to generate output files for "rule all" are defined in the common.smk file
 rule all:
     input: