minor changes in Snakemake file

Snakefile

-# File for running ONT analyses
+# Pipeline
 
 ##############################
 # MODULES
@@ -7,7 +7,8 @@ from tempfile import TemporaryDirectory
 
 ##############################
 # CONFIG
-# configfile:"config/CONFIG.yaml"
+# can be overwritten by using --configfile <path to config> when calling snakemake
+configfile: "config/CONFIG.yaml"
 
 # Paths
 SRC_DIR = srcdir("workflow/scripts")
@@ -45,12 +46,16 @@ shell.executable("bash")
 
 # working directory
 workdir:
-        config["work_dir"]
+    config["work_dir"]
 
-# include rules for the workflows based on "steps" in the CONFIG.yaml file
-# ONT analyses workflow
+##############################
+# TARGETS & RULES
+# List of targets to be created
 TARGETS = []
 
+# Include rules and add targets based on the config file
+
+# Assembly annotation
 if 'assembly_annotation' in STEPS:
     include:
         "workflow/steps/assembly_annotation.smk"
@@ -77,6 +82,7 @@ if 'checkpoint_assembly_annotation' in STEPS:
         "dummy_folders_created.done"
     ]
 
+# MMSEQ2
 if 'mmseq' in STEPS:
     include:
         "workflow/steps/mmseq.smk"
@@ -84,26 +90,31 @@ if 'mmseq' in STEPS:
         "mmseq_comparison_for_ont.done"
     ]
 
+# MetaT
 if 'metaT' in STEPS:
     include:
         "workflow/steps/metat.smk"
     TARGETS += ["metaT_mapping_for_ONT.done"]
 
+# Mapping
 if 'mapping' in STEPS:
     include:
         "workflow/steps/mapping.smk"
     TARGETS += ["mapping_for_binning.done"]
 
+# Binning
 if 'binning' in STEPS:
     include:
         "workflow/steps/binning.smk"
     TARGETS += ["binning_for_ont.done"]
 
+# Taxonomy
 if 'taxonomy' in STEPS:
     include:
         "workflow/steps/taxonomy.smk"
     TARGETS += ["taxonomy_for_ont.done"]
 
+# Analysis
 if 'analysis' in STEPS:
     include:
         "workflow/steps/analysis.smk"
@@ -123,9 +134,9 @@ if 'analysis' in STEPS:
     if "amr" in ANALYSIS_STEPS:
         TARGETS.append("amr_analysis.done")
 
-#else:
-#    raise Exception('You are not serious. No input data')
-#        print("No input data provided")
+# No targets
+if len(TARGETS) == 0:
+   raise Exception('You are not serious. Nothing to be done? Really?')
 
 rule all:
     input: