DADA2 makeSequenceTable

dada2.smk

@@ -7,3 +7,13 @@ rule dada2:
 		config["THREADS"]
 	script:
 		"dada2.R"
+
+rule makeSequenceTable:
+	input:
+		expand("work/dada/{sample}.rds", sample=SAMPLES)
+	output:
+		"work/dada/seqtab.rds"
+	threads:
+		config["THREADS"]
+	script:
+		"makeSequenceTable.R"

global.smk

@@ -6,7 +6,8 @@ SAMPLES=config["SAMPLES"]
 rule all:
 	input:
 		"report/multiqc_report.html",
-		expand("work/dada/{sample}.rds", sample=SAMPLES)
+		expand("work/dada/{sample}.rds", sample=SAMPLES),
+		"work/dada/seqtab.rds"
 
 include: "quality.smk"
 include: "preprocess.smk"

makeSequenceTable.R

+library(dada2)
+
+seqtab <- makeSequenceTable(lapply(snakemake@input, readRDS), orderBy = "abundance")
+seqtab.nochim <- removeBimeraDenovo(seqtab, method="consensus", multithread = snakemake@threads, verbose = TRUE)
+saveRDS(seqtab.nochim, snakemake@output[[1]])