adjusted paths to scripts in rules (issue #15)

rules/AMR/Combine_MGE_AMR

@@ -26,7 +26,7 @@ rule combine_AMR_plasmid:
 		Report_2=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_report_temp.csv")
 	params: outdir="{OUTDIR}"
 	conda: "../../envs/R.yaml"
-	script: "AMR_MGE.R"
+	script: "../../scripts/AMR_MGE.R"
 
 rule modify_details:
 	input:"{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.csv"

rules/Toxin/Combine_Toxin_SignalP

@@ -24,7 +24,7 @@ rule R_script:
     message: "Run external R script to join SignalP and ToxinHMM"
     params: outdir="{OUTDIR}"
     conda: "../../envs/R.yaml"
-    script: "ownHMM_library.R"
+    script: "../../scripts/ownHMM_library.R"
 
 #Put the different files in the correct configuration
 ###Gene table library

rules/Universal/Combine_PathoFact

@@ -14,7 +14,7 @@ rule combine_PathoFact:
 		AMR_MGE="{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv"
 	output: "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
 	conda: "../../envs/R.yaml"
-	script: "PathoFact.R"
+	script: "../../scripts/PathoFact.R"
 
 
 

rules/Virulence/Virulence

@@ -56,7 +56,7 @@ rule HMM_R_VIR:
                 ID="{OUTDIR}/{project}/renamed/{input_file}_translation.tsv"
         output: "{OUTDIR}/{project}/VIRULENCE/HMM_virulence/{input_file}.hmm_results.csv"
         conda: "../../envs/R.yaml"
-        script: "hmm.R"
+        script: "../../scripts/hmm.R"
 
 
 ## Give pathogenicity prediction