Delete preprocess.smk

workflow/rules/preprocess.smk

-rule cutadapt:
-	input:
-		"DATA/{sample}.fastq.gz"
-	output:
-		"work/cutadapt/{sample}.fastq.gz"
-	params:
-		five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
-		three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
-	shell:
-		"conda activate cutadapt-2.5 "
-		"&& "
-		"cutadapt "
-		"-g {params.five} "
-		"-a {params.three} "
-		"--error-rate 0.1 "
-		"--discard-untrimmed "
-		"--match-read-wildcards "
-		"-o {output} "
-		"{input} "
-		"&& "
-		"conda deactivate"
-
-rule filter:
-	input:
-		"work/cutadapt/{sample}.fastq.gz"
-	output:
-		"work/filter/{sample}.fastq.gz"
-	script:
-		"filterAndTrim.R"