updated step mmseq and Snakemake file

Snakefile

@@ -65,7 +65,7 @@ if 'assembly_annotation' in STEPS:
 
 if 'checkpoint_assembly_annotation' in STEPS:
     include:
-        "workflows/checkpoint_assembly_annotation.smk"
+        "workflow/steps/checkpoint_assembly_annotation.smk"
     TARGETS += [
         "assemble_and_coverage.done",
         "annotate.done",
@@ -77,10 +77,12 @@ if 'checkpoint_assembly_annotation' in STEPS:
         "dummy_folders_created.done"
     ]
 
-# if 'mmseq' in STEPS:
-#     include:
-#         "workflows/mmseq.smk"
-#     TARGETS += ["mmseq_comparison_for_ont.done"]
+if 'mmseq' in STEPS:
+    include:
+        "workflow/steps/mmseq.smk"
+    TARGETS += [
+        "mmseq_comparison_for_ont.done"
+    ]
 
 # if 'metaT' in STEPS:
 #     include:

workflow/steps/mmseq.smk

@@ -2,7 +2,7 @@
 
 # specify which rules to run
 include:
-    '../rules/MMSEQ_RULES'
+    '../rules/mmseq.smk'
 
 # Rule all for running the MMSEQ2 analyses on the proteins after assembly
 rule MMSEQ: