quality

config.json

 {
 	"THREADS": 8,
-	"MEM": 10
+	"MEM": 10,
+	"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"]
 }

global.smk

+configfile: "./config.json"
+
+MEM=config["MEM"]
+SAMPLES=config["SAMPLES"]
+
+rule all:
+	input:
+		"report/multiqc_report.html"
+
+include: "quality.smk"

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:
+		"fastqc "
+		"{input} "
+		"--noextract "
+		"--outdir {params.output} "
+
+rule multiqc:
+	input:
+		expand("work/fastqc/{sample}_fastqc.zip", sample=SAMPLES)
+	output:
+		html = "report/multiqc_report.html",
+	params:
+		output = "report/"
+	shell:
+		"multiqc "
+		"--no-data-dir "
+		"--outdir {params.output} "
+		"{input} "