added workflow parameter to config.yaml and updated Snakefile (issue #24)

Snakefile

 #Snakefile
 
-w = 'complete'
-
-if w is 'complete':
+if config["workflow"] == "complete":
     include:
         "workflows/Combine_PathoFact_workflow"
     rule all:
@@ -15,7 +13,7 @@ if w is 'complete':
                 ],
                 OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
             )
-elif w is 'Tox':
+elif config["workflow"] == "Tox":
     include:
         "workflows/Toxin_workflow"
     rule all:
@@ -27,7 +25,7 @@ elif w is 'Tox':
                 ],
                 OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
             )
-elif w is 'Vir':
+elif config["workflow"] == "Vir":
     include:
         "workflows/Virulence_workflow"
     rule all:
@@ -36,7 +34,7 @@ elif w is 'Vir':
                 "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
                 OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
             )                    
-elif w is 'AMR':
+elif config["workflow"] == "AMR":
     include:
         "workflows/AMR_workflow"
     rule all:
@@ -49,4 +47,4 @@ elif w is 'AMR':
                 OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
             )
 else:
-    raise Exception('NO workflow selected')
+    raise Exception("Unknown workflow option: %s" % config["workflow"])

config.yaml

@@ -12,6 +12,13 @@ OUTDIR: /path/to/samples
 # Define size of split fasta files (default 10 000 sequences/file)
 size_fasta: 100000
 
+# Workflow (default: "complete")
+# complete: complete pipeline: toxin + virulence + (AMR + MGE) prediction
+# Tox:      toxin prediction
+# Vir:      virulence prediction
+# AMR:      antimicrobial resistance (AMR) & mobile genetic element (MGE) prediction
+workflow: "complete"
+
 ###########    
 # SignalP #
 ###########