format fix in workflow files (issue #26)

workflows/AMR_workflow

 config: "config.yaml"
 # include rules for the Analysis part of the workflow
 include:
-	'../rules/Universal/Preprocessing'
+    '../rules/Universal/Preprocessing'
 include:
-	'../rules/Universal/Preprocessing_contig'
+    '../rules/Universal/Preprocessing_contig'
 include:
-	'../rules/AMR/AMR'
+    '../rules/AMR/AMR'
 include:
-	'../rules/AMR/Plasmid'
+    '../rules/AMR/Plasmid'
 include:
-	'../rules/AMR/Phage'
+    '../rules/AMR/Phage'
 include:
-	'../rules/AMR/Combine_MGE_AMR'
+    '../rules/AMR/Combine_MGE_AMR'
 
 # master command
 rule AMR_Analysis:
-	input: 
-		expand(["{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv",
-			"{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
-			"{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv", 
-			"{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"])
-	output:
-		touch('AMR_analyis.done')
+    input: 
+        expand(
+            [
+                "{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv",
+                "{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
+                "{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv", 
+                "{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"]
+        )
+    output:
+        touch('AMR_analyis.done')

workflows/Combine_PathoFact_workflow

 # include rules for the Analysis part of the workflow
 include:
-        '../rules/Universal/Preprocessing'
+    '../rules/Universal/Preprocessing'
 include:
-        '../rules/Universal/SignalP'
+    '../rules/Universal/SignalP'
 include:
-        '../rules/Virulence/Virulence'
+    '../rules/Virulence/Virulence'
 include:
-        '../rules/Virulence/Combine_Virulence_SignalP'
+    '../rules/Virulence/Combine_Virulence_SignalP'
 include:
-        '../rules/Virulence/Virulence_report'
+    '../rules/Virulence/Virulence_report'
 include:
-        '../rules/Toxin/Toxin'
+    '../rules/Toxin/Toxin'
 include:
-        '../rules/Toxin/Combine_Toxin_SignalP'
+    '../rules/Toxin/Combine_Toxin_SignalP'
 include:
-        '../rules/Toxin/Toxin_report'
+    '../rules/Toxin/Toxin_report'
 include:
-        '../rules/Universal/Preprocessing_contig'
+    '../rules/Universal/Preprocessing_contig'
 include:
-        '../rules/AMR/AMR'
+    '../rules/AMR/AMR'
 include:
-        '../rules/AMR/Plasmid'
+    '../rules/AMR/Plasmid'
 include:
-        '../rules/AMR/Phage'
+    '../rules/AMR/Phage'
 include:
-        '../rules/AMR/Combine_MGE_AMR'
+    '../rules/AMR/Combine_MGE_AMR'
 include:
-	'../rules/Universal/Combine_PathoFact'
+    '../rules/Universal/Combine_PathoFact'
 
 # master command
 rule Analysis:
-        input:
-                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"])
-        output:
-                touch('PathoFact_analyis.done')
+    input:
+        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"]
+        )
+    output:
+        touch('PathoFact_analyis.done')

workflows/Toxin_workflow

 # include rules for the Analysis part of the workflow
 include:
-	'../rules/Universal/Preprocessing'
+    '../rules/Universal/Preprocessing'
 include:
-        '../rules/Universal/SignalP'
+    '../rules/Universal/SignalP'
 include:
-	'../rules/Toxin/Toxin'
+    '../rules/Toxin/Toxin'
 include:
-	'../rules/Toxin/Combine_Toxin_SignalP'
+    '../rules/Toxin/Combine_Toxin_SignalP'
 include:
-	'../rules/Toxin/Toxin_report'
+    '../rules/Toxin/Toxin_report'
 
 # master command
 rule Analysis:
-        input:
-                expand(["{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
-		"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
-		"{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv"], OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-        output:
-                touch('Toxin_analyis.done')
+    input:
+        expand(
+            [
+                "{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
+                "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
+                "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv"
+            ],
+            OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+        )
+    output:
+        touch('Toxin_analyis.done')

workflows/Virulence_workflow

 # include rules for the Analysis part of the workflow
 include:
-	'../rules/Universal/Preprocessing'
+    '../rules/Universal/Preprocessing'
 include:
-        '../rules/Universal/SignalP'
+    '../rules/Universal/SignalP'
 include:
-	'../rules/Virulence/Virulence'
+    '../rules/Virulence/Virulence'
 include:
-	'../rules/Virulence/Combine_Virulence_SignalP'
+    '../rules/Virulence/Combine_Virulence_SignalP'
 include:
-	'../rules/Virulence/Virulence_report'
+    '../rules/Virulence/Virulence_report'
 
 # master command
 rule Analysis_Virulence:
-        input:
-                expand(["{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
-			"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv"],
-			OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
-        output:
-                touch('virulence_analyis.done')
-
+    input:
+        expand(
+            [
+                "{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
+                "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv"
+            ],
+            OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+        )
+    output:
+        touch('virulence_analyis.done')