DADA2 filterAndTrim

filterAndTrim.R

+library(dada2)
+
+filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)

preprocess.smk

@@ -15,3 +15,11 @@ rule cutadapt:
         "--match-read-wildcards " 
         "-o {output} " 
         "{input} "
+
+rule filter:
+	input:
+		"work/cutadapt/{sample}.fastq.gz"
+	output:
+		"work/filter/{sample}.fastq.gz"
+	script:
+		"filterAndTrim.R"