format fix in Snakefile (issue #26)

Snakefile

@@ -7,36 +7,46 @@ if w is 'complete':
         "workflows/Combine_PathoFact_workflow"
     rule all:
         input:
-                        expand(["{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
+            expand(
+                [
+                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
                     "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
-                                "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"],
-                                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-
+                    "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
+                ],
+                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+            )
 elif w is 'Tox':
     include:
         "workflows/Toxin_workflow"
     rule all:
         input:
-                        expand(["{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
-                                "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"],
-                                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-
+            expand(
+                [
+                    "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
+                    "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"
+                ],
+                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+            )
 elif w is 'Vir':
     include:
         "workflows/Virulence_workflow"
     rule all:
         input:
-                        expand("{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
-                                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-                                
+            expand(
+                "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
+                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+            )                    
 elif w is 'AMR':
     include:
         "workflows/AMR_workflow"
     rule all:
         input:
-                        expand(["{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
-                                "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"],
-                                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-
+            expand(
+                [
+                    "{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
+                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
+                ],
+                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+            )
 else:
     raise Exception('NO workflow selected')