Print an immediate error if no input samples were found.

Also clean up the comment and remove unused glob import.

workflow/Snakefile

@@ -1,21 +1,14 @@
-# Main entrypoint of the workflow.
-# Please follow the best practices:
+# Main Snakefile and entry point of the workflow.
+# Please see the best practices:
 # https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html,
 # in particular regarding the standardized folder structure mentioned there.
 
-
-# Main Snakefile
-
-
 # set config file where you can specify your inputs
 configfile: "config/config.yaml"
 
-
-# import glob to read {sample}
-import glob
-
 # set {samples} wildcard
-samples = glob_wildcards(config["hic_path"] + "{sample}_1.fastq.gz").sample
+samples_in_pattern = "{sample}_1.fastq.gz"
+samples = glob_wildcards(config["hic_path"] + samples_in_pattern).sample
 
 
 # Include the hifi_prep rule
@@ -58,4 +51,4 @@ include: "rules/common.smk"
 # input files are defined in the common.smk file
 rule all:
     input:
-        get_all_inputs(),
+        get_all_inputs

workflow/rules/common.smk

@@ -1,8 +1,14 @@
 # Define function for the inputs to rule_all
 # this rule just defines the inputs to the final rule
 
+def get_all_inputs(wc=None):
+    if not samples:
+        # Show the user a meaningful error message
+        logger.error(f"No files matching {samples_in_pattern} were found in"
+                     f" {config.get('hic_path')}. Please check your config file.")
+        logger.error(f"Exiting.")
+        sys.exit(1)
 
-def get_all_inputs():
     inputs = [
         "results/reads/hifi/hifi.fastq.gz",  # output of hifi_prep rule
         "results/nanoplot/NanoPlot-report.html",  # nanoplot report