updated step analysis

Snakefile

@@ -10,8 +10,8 @@ from tempfile import TemporaryDirectory
 # configfile:"config/CONFIG.yaml"
 
 # Paths
-SRC_DIR = srcdir("scripts")
-ENV_DIR = srcdir("envs")
+SRC_DIR = srcdir("workflow/scripts")
+ENV_DIR = srcdir("workflow/envs")
 DATA_DIR = config["data_dir"]
 RESULTS_DIR = config["results_dir"]
 DB_DIR = config["db_dir"]
@@ -104,24 +104,24 @@ if 'taxonomy' in STEPS:
         "workflow/steps/taxonomy.smk"
     TARGETS += ["taxonomy_for_ont.done"]
 
-# if 'analysis' in STEPS:
-#     include:
-#         "workflows/analysis.smk"
-#     # CD-HIT
-#     if "cdhit" in ANALYSIS_STEPS:
-#         TARGETS.append("cdhit_analysis.done")
-#     # Mappability
-#     if "mappability" in ANALYSIS_STEPS:
-#         TARGETS.append("mappability_index.done")
-#     # CRISPR
-#     if "crispr" in ANALYSIS_STEPS:
-#         TARGETS.append("crispr_analysis.done")
-#     # Plasmid prediction
-#     if "plasmids" in ANALYSIS_STEPS:
-#         TARGETS.append("plasmids_analysis.done")
-#     # AMR prediction
-#     if "amr" in ANALYSIS_STEPS:
-#         TARGETS.append("amr_analysis.done")
+if 'analysis' in STEPS:
+    include:
+        "workflow/steps/analysis.smk"
+    # CD-HIT
+    if "cdhit" in ANALYSIS_STEPS:
+        TARGETS.append("cdhit_analysis.done")
+    # Mappability
+    if "mappability" in ANALYSIS_STEPS:
+        TARGETS.append("mappability_index.done")
+    # CRISPR
+    if "crispr" in ANALYSIS_STEPS:
+        TARGETS.append("crispr_analysis.done")
+    # Plasmid prediction
+    if "plasmids" in ANALYSIS_STEPS:
+        TARGETS.append("plasmids_analysis.done")
+    # AMR prediction
+    if "amr" in ANALYSIS_STEPS:
+        TARGETS.append("amr_analysis.done")
 
 #else:
 #    raise Exception('You are not serious. No input data')

workflow/steps/analysis.smk

@@ -2,7 +2,7 @@
 
 # specify which rules to run
 include:
-    '../rules/ANALYSIS_RULES'
+    '../rules/analysis.smk'
 
 # Rule all for running the analysing partial gene counts in prodigal and unique gene counts with cd-hit on the proteins
 rule CDHIT: