updated init.smk and main Snakefile (tax is switched off)

workflow/Snakefile

@@ -34,7 +34,7 @@ include:
 # TARGETS.append("status/prepare_input.done") # TEST
 
 # Preprocessing
-if "preprocessing" in STEPS:
+if "preprocessing" in config['steps']:
     include:
         "steps/preprocessing.smk"
     TARGETS += [
@@ -43,7 +43,7 @@ if "preprocessing" in STEPS:
     ]
 
 # Assembly
-if "assembly" in STEPS:
+if "assembly" in config['steps']:
     include:
         "steps/assembly.smk"
     TARGETS += [
@@ -51,7 +51,7 @@ if "assembly" in STEPS:
     ]
 
 # Assembly mapping
-if "mapping" in STEPS:
+if "mapping" in config['steps']:
     include:
         "steps/mapping.smk"
     TARGETS += [
@@ -61,7 +61,7 @@ if "mapping" in STEPS:
     ]
 
 # Assembly annotation
-if "annotation" in STEPS:
+if "annotation" in config['steps']:
     include:
         "steps/annotation.smk"
     TARGETS += [
@@ -69,20 +69,20 @@ if "annotation" in STEPS:
     ]
 
 # Analysis
-if "analysis" in STEPS:
+if "analysis" in config['steps']:
     include:
         "steps/analysis.smk"
     TARGETS += [
         "status/analysis.done"
     ]
 
-# Taxonomy
-if "taxonomy" in STEPS:
-    include:
-        "steps/taxonomy.smk"
-    TARGETS += [
-        "status/taxonomy.done"
-    ]
+# # Taxonomy
+# if "taxonomy" in config['steps']:
+#     include:
+#         "steps/taxonomy.smk"
+#     TARGETS += [
+#         "status/taxonomy.done"
+#     ]
 
 # No targets
 if len(TARGETS) == 0:

workflow/rules/init.smk

@@ -17,7 +17,7 @@ RESULTS_DIR = config["results_dir"]
 DB_DIR = config["db_dir"]
 
 # Steps
-STEPS               = config['steps']
+# STEPS = config['steps']
 
 # Input
 # INPUT_G_LR_FAST5 = find_fast5(config["data"]["metag"]["ont"]["files"], config["data"]["metag"]["ont"]["dirs"])