rule clean_files:
	input: "{sample}/profiles/{database}/{tool}.profile.out"
	output: touch("{sample}/profiles/{database}/{tool}_clean_files.done")
	log: "{sample}/log/{database}/{tool}_clean_files.log"
	benchmark: "{sample}/log/{database}/{tool}_clean_files.time"
	run:
		if not config["keepfiles"]: 
			# Remove individual folder (sample/tool/database)
			shell("rm -rfv {wildcards.sample}/{wildcards.tool}/{wildcards.database}/ > {log} 2>&1")
			# Remove tool folder if it existst and there's no more data (sample/tool)
			shell('if [ -d "{wildcards.sample}/{wildcards.tool}/" ]; then if [ ! "$(ls -A {wildcards.sample}/{wildcards.tool}/)" ]; then rm -rfv {wildcards.sample}/{wildcards.tool}/ >> {log} 2>&1; fi; fi')