rm configfile from all snakemake files except Snakefile (issue #25)

Snakefile

 #Snakefile
 
+# can be overwritten by using --configfile <config file> when calling snakemake
+configfile: "config.yaml"
+
 if config["workflow"] == "complete":
     include:
         "workflows/Combine_PathoFact_workflow"

rules/AMR/AMR.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile:"config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/AMR/Combine_MGE_AMR.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile:"config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/AMR/Phage.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/AMR/Plasmid.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Toxin/Combine_Toxin_SignalP.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Toxin/Toxin.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Toxin/Toxin_report.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Universal/Combine_PathoFact.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Universal/Preprocessing.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Universal/Preprocessing_contig.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Universal/SignalP.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Virulence/Combine_Virulence_SignalP.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Virulence/Virulence.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

rules/Virulence/Virulence_report.snk

@@ -3,7 +3,6 @@
 import glob
 import os
 
-configfile: "config.yaml"
 PROJECT = config["project"]
 INPUT   = config["input_file"]
 

workflows/AMR_workflow.snk

-config: "config.yaml"
 # include rules for the Analysis part of the workflow
 include:
     '../rules/Universal/Preprocessing'