DADA2 biom

dada2.smk

@@ -14,7 +14,8 @@ rule makeSequenceTable:
 	output:
 		rds = "work/dada/seqtab.rds",
 		fasta = "work/dada/seqtab.fasta",
-		tsv = "work/dada/seqtab.tsv"
+		tsv = "work/dada/seqtab.tsv",
+		biom = "work/dada/dada.biom"
 	threads:
 		config["THREADS"]
 	script:

makeSequenceTable.R

 library(dada2)
+library(biomformat)
 
 dada_list <- lapply(snakemake@input, readRDS)
 names(dada_list) <- lapply(snakemake@input, function(x){basename(tools::file_path_sans_ext(x))})
@@ -11,3 +12,6 @@ saveRDS(seqtab.nochim, snakemake@output$rds)
 uniquesToFasta(seqtab.nochim, snakemake@output$fasta)
 
 write.table(t(seqtab.nochim), snakemake@output$tsv, sep = "\t", quote = FALSE)
+
+biom <- make_biom(t(seqtab.nochim))
+write_biom(biom, snakemake@output$biom)