rule download_samples:
	output: "DATA/paired/{sample}/{sample}.sra"
	log: "00_logs/{sample}_download_data.log"
	shell: "prefetch {wildcards.sample} -O 'DATA/paired/' 2> '{log}'"

rule sra_to_fastq:
	input: "DATA/paired/{sample}/{sample}.sra"
	output:
		"DATA/paired/{sample}_1.fastq.gz",
		"DATA/paired/{sample}_2.fastq.gz"
	log: "00_logs/{sample}_sra_to_fastq.log"
	shell: """
	fasterq-dump '{input}' --split-files --outdir 'DATA/paired/' 2> '{log}'
	gzip 'DATA/paired/{wildcards.sample}_1.fastq'
	gzip 'DATA/paired/{wildcards.sample}_2.fastq'
	"""
	
rule link_reads:
	input:
		r1 = "DATA/paired/{sample}_1.fastq.gz",
		r2 = "DATA/paired/{sample}_2.fastq.gz"
	output:
		o1 = "01_raw_data/{sample}_1.fastq.gz",
		o2 = "01_raw_data/{sample}_2.fastq.gz"
	log: "00_logs/{sample}_link_reads.log"
	run:
		shell("ln -sf '{input.r1}' '{output.o1}'")
		shell("ln -sf '{input.r2}' '{output.o2}'")
