rule align_reads:
	input:
		genome = multiext("01_raw_data/GENOME", ".amb", ".ann", ".bwt", ".pac", ".sa"),
		r1 = "01_raw_data/{sample}_1.fastq.gz",
		r2 = "01_raw_data/{sample}_2.fastq.gz"
	output: "03_sam_files/{sample}.sam"
	log: "00_logs/{sample}_align_reads_err.log"
	resources:
		mem_mb = 1024 * 50, # Last number is memory in GB
		time = 60 * 24 * 3, # Last number is days
		#account = "publicgrp", # Placeholder for SLURM submission
		#partition = "high", # Placeholder for SLURM submission
	shell:
		"bwa mem -t THREADS '01_raw_data/GENOME' '{input.r1}' '{input.r2}' > '{output}' "
		"2> '{log}'"
