no biom, tsv export

dada2.smk

@@ -12,9 +12,9 @@ rule makeSequenceTable:
 	input:
 		expand("work/dada/{sample}.rds", sample=SAMPLES)
 	output:
-		table = "work/dada/seqtab.rds",
+		rds = "work/dada/seqtab.rds",
 		fasta = "work/dada/seqtab.fasta",
-		biom = "work/dada/dada2.biom"
+		tsv = "work/dada/seqtab.tsv"
 	threads:
 		config["THREADS"]
 	script:

global.smk

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

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))})
@@ -7,9 +6,8 @@ names(dada_list) <- lapply(snakemake@input, function(x){basename(tools::file_pat
 seqtab <- makeSequenceTable(dada_list, orderBy = "abundance")
 seqtab.nochim <- removeBimeraDenovo(seqtab, method="consensus", multithread = snakemake@threads, verbose = TRUE)
 
-saveRDS(seqtab.nochim, snakemake@output$table)
+saveRDS(seqtab.nochim, snakemake@output$rds)
 
 uniquesToFasta(seqtab.nochim, snakemake@output$fasta)
 
-biom <- make_biom(t(seqtab.nochim))
-write_biom(biom, snakemake@output$biom)
+write.table(t(seqtab.nochim), snakemake@output$tsv, sep = "\t", quote = FALSE)