*.snk to *.smk in files (issue #18)

Snakefile

@@ -5,7 +5,7 @@ configfile: "config.yaml"
 
 if config["workflow"] == "complete":
     include:
-        "workflows/Combine_PathoFact_workflow.snk"
+        "workflows/Combine_PathoFact_workflow.smk"
     rule all:
         input:
             expand(
@@ -18,7 +18,7 @@ if config["workflow"] == "complete":
             )
 elif config["workflow"] == "Tox":
     include:
-        "workflows/Toxin_workflow.snk"
+        "workflows/Toxin_workflow.smk"
     rule all:
         input:
             expand(
@@ -30,7 +30,7 @@ elif config["workflow"] == "Tox":
             )
 elif config["workflow"] == "Vir":
     include:
-        "workflows/Virulence_workflow.snk"
+        "workflows/Virulence_workflow.smk"
     rule all:
         input:
             expand(
@@ -39,7 +39,7 @@ elif config["workflow"] == "Vir":
             )                    
 elif config["workflow"] == "AMR":
     include:
-        "workflows/AMR_workflow.snk"
+        "workflows/AMR_workflow.smk"
     rule all:
         input:
             expand(

workflows/AMR_workflow.smk

 # include rules for the Analysis part of the workflow
 include:
-    '../rules/Universal/Preprocessing.snk'
+    '../rules/Universal/Preprocessing.smk'
 include:
-    '../rules/Universal/Preprocessing_contig.snk'
+    '../rules/Universal/Preprocessing_contig.smk'
 include:
-    '../rules/AMR/AMR.snk'
+    '../rules/AMR/AMR.smk'
 include:
-    '../rules/AMR/Plasmid.snk'
+    '../rules/AMR/Plasmid.smk'
 include:
-    '../rules/AMR/Phage.snk'
+    '../rules/AMR/Phage.smk'
 include:
-    '../rules/AMR/Combine_MGE_AMR.snk'
+    '../rules/AMR/Combine_MGE_AMR.smk'
 
 # master command
 rule AMR_Analysis:

workflows/Combine_PathoFact_workflow.smk

 # include rules for the Analysis part of the workflow
 include:
-    '../rules/Universal/Preprocessing.snk'
+    '../rules/Universal/Preprocessing.smk'
 include:
-    '../rules/Universal/SignalP.snk'
+    '../rules/Universal/SignalP.smk'
 include:
-    '../rules/Virulence/Virulence.snk'
+    '../rules/Virulence/Virulence.smk'
 include:
-    '../rules/Virulence/Combine_Virulence_SignalP.snk'
+    '../rules/Virulence/Combine_Virulence_SignalP.smk'
 include:
-    '../rules/Virulence/Virulence_report.snk'
+    '../rules/Virulence/Virulence_report.smk'
 include:
-    '../rules/Toxin/Toxin.snk'
+    '../rules/Toxin/Toxin.smk'
 include:
-    '../rules/Toxin/Combine_Toxin_SignalP.snk'
+    '../rules/Toxin/Combine_Toxin_SignalP.smk'
 include:
-    '../rules/Toxin/Toxin_report.snk'
+    '../rules/Toxin/Toxin_report.smk'
 include:
-    '../rules/Universal/Preprocessing_contig.snk'
+    '../rules/Universal/Preprocessing_contig.smk'
 include:
-    '../rules/AMR/AMR.snk'
+    '../rules/AMR/AMR.smk'
 include:
-    '../rules/AMR/Plasmid.snk'
+    '../rules/AMR/Plasmid.smk'
 include:
-    '../rules/AMR/Phage.snk'
+    '../rules/AMR/Phage.smk'
 include:
-    '../rules/AMR/Combine_MGE_AMR.snk'
+    '../rules/AMR/Combine_MGE_AMR.smk'
 include:
-    '../rules/Universal/Combine_PathoFact.snk'
+    '../rules/Universal/Combine_PathoFact.smk'
 
 # master command
 rule Analysis:

workflows/Toxin_workflow.smk

 # include rules for the Analysis part of the workflow
 include:
-    '../rules/Universal/Preprocessing.snk'
+    '../rules/Universal/Preprocessing.smk'
 include:
-    '../rules/Universal/SignalP.snk'
+    '../rules/Universal/SignalP.smk'
 include:
-    '../rules/Toxin/Toxin.snk'
+    '../rules/Toxin/Toxin.smk'
 include:
-    '../rules/Toxin/Combine_Toxin_SignalP.snk'
+    '../rules/Toxin/Combine_Toxin_SignalP.smk'
 include:
-    '../rules/Toxin/Toxin_report.snk'
+    '../rules/Toxin/Toxin_report.smk'
 
 # master command
 rule Analysis:

workflows/Virulence_workflow.smk

 # include rules for the Analysis part of the workflow
 include:
-    '../rules/Universal/Preprocessing.snk'
+    '../rules/Universal/Preprocessing.smk'
 include:
-    '../rules/Universal/SignalP.snk'
+    '../rules/Universal/SignalP.smk'
 include:
-    '../rules/Virulence/Virulence.snk'
+    '../rules/Virulence/Virulence.smk'
 include:
-    '../rules/Virulence/Combine_Virulence_SignalP.snk'
+    '../rules/Virulence/Combine_Virulence_SignalP.smk'
 include:
-    '../rules/Virulence/Virulence_report.snk'
+    '../rules/Virulence/Virulence_report.smk'
 
 # master command
 rule Analysis_Virulence: