cutadapt

config.json

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

global.smk

@@ -8,3 +8,4 @@ rule all:
 		"report/multiqc_report.html"
 
 include: "quality.smk"
+include: "preprocess.smk"

preprocess.smk

+rule cutadapt:
+    input:
+        "DATA/{sample}.fastq.gz" 
+    output:
+        "work/cutadapt/{sample}.fastq.gz" 
+    params:
+    	five = config["FIVE_PRIMER"],
+    	three = config["THREE_PRIMER"]
+    shell:
+        "cutadapt "
+        "-g {params.five} "
+        "-a {params.three} "
+        "--error-rate 0.1 " 
+        "--discard-untrimmed " 
+        "--match-read-wildcards " 
+        "-o {output} " 
+        "{input} "