DADA2

dada2.R

+library(dada2)
+
+derep <- derepFastq(snakemake@input[[1]], verbose = TRUE)
+err <- learnErrors(snakemake@input[[1]], multithread = snakemake@threads, verbose = TRUE)
+dada <- dada(derep, err = err, multithread = snakemake@threads, verbose = TRUE)
+saveRDS(dada, snakemake@output[[1]])

dada2.smk

+rule dada2:
+	input:
+		"work/filter/{sample}.fastq.gz"
+	output:
+		"work/dada/{sample}.rds"
+	threads:
+		config["THREADS"]
+	script:
+		"dada2.R"

global.smk

@@ -5,7 +5,9 @@ SAMPLES=config["SAMPLES"]
 
 rule all:
 	input:
-		"report/multiqc_report.html"
+		"report/multiqc_report.html",
+		expand("work/dada/{sample}.rds", sample=SAMPLES)
 
 include: "quality.smk"
 include: "preprocess.smk"
+include: "dada2.smk"