Update PathoFact.R

rules/Universal/PathoFact.R

@@ -24,7 +24,7 @@ colnames(AMR_MGE) <- c("GeneID","Gene_Name","Contig_Name","ARG_prediction","AMR_
 Predictions_dfs<-list(Toxins, Virulence_factors, AMR_MGE)
 PathoFact_predictions<-Reduce(full_join, Predictions_dfs)
 PathoFact_predictions <- PathoFact_predictions[,c(1,7,8,3,2,4,5,6,9,10,11)]
+PathoFact_predictions <- PathoFact_predictions %>% filter(GeneID != "        NA")
 write.csv(PathoFact_predictions, file=snakemake@output[[1]], row.names=FALSE)
 
 
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