Delete quality.smk

workflow/rules/quality.smk

-rule fastqc:
-	input:
-		"DATA/{sample}.fastq.gz"
-	output:
-		zip = "work/fastqc/{sample}_fastqc.zip",
-		html = "work/fastqc/{sample}_fastqc.html"
-	params:
-		output = "work/fastqc/"
-	shell:
-		"conda activate fastqc-0.11.8 "
-		"&& "
-		"fastqc "
-		"{input} "
-		"--noextract "
-		"--outdir {params.output} "
-		"&& "
-		"conda deactivate "
-
-rule multiqc:
-	input:
-		expand("work/fastqc/{sample}_fastqc.zip", sample=SAMPLES)
-	output:
-		html = "report/multiqc_report.html",
-	params:
-		output = "report/"
-	shell:
-		"conda activate multiqc-1.8 "
-		"&& "
-		"multiqc "
-		"--no-data-dir "
-		"--outdir {params.output} "
-		"{input} "
-		"&& "
-		"conda deactivate "