output directory check: address case in which file with same name exists
output directory check: address case in which file with same name exists

satta/companion,satta/companion,satta/annot-nf,sanger-pathogens/companion,sanger-pathogens/annot-nf,sanger-pathogens/annot-nf,sanger-pathogens/annot-nf,satta/companion,sanger-pathogens/companion,satta/annot-nf,satta/annot-nf,sanger-pathogens/companion