rule align_reads:
	input:
		genome = multiext("01_raw_data/GENOME", ".1.bt2", ".2.bt2", ".3.bt2", ".4.bt2",
			".rev.1.bt2", ".rev.2.bt2"),
		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:
		"bowtie2 -p THREADS -x '01_raw_data/GENOME' -1 '{input.r1}' -2 '{input.r2}' "
		"> '{output}' 2> '{log}'"
