rule markdup:
	input: "04_bam_files/{sample}.sorted.fixmate.bam"
	output: "04_bam_files/{sample}.sorted.dedup.bam"
	log: "00_logs/{sample}_sam_markdup.log"
	shell:
		"""
		picard MarkDuplicates -REMOVE_DUPLICATES true -I '{input}' -M '{wildcards.sample}.dup_metrics' -O '{output}' 2> '{log}'
		mv '{wildcards.sample}.dup_metrics' 04_bam_files/
		"""