fasta export

dada2.smk

@@ -12,7 +12,8 @@ rule makeSequenceTable:
 	input:
 		expand("work/dada/{sample}.rds", sample=SAMPLES)
 	output:
-		"work/dada/seqtab.rds"
+		table = "work/dada/seqtab.rds",
+		fasta = "work/dada/seqtab.fasta"
 	threads:
 		config["THREADS"]
 	script:

global.smk

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

makeSequenceTable.R

@@ -2,4 +2,5 @@ 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]])
+saveRDS(seqtab.nochim, snakemake@output$table)
+uniquesToFasta(seqtab.nochim, snakemake@output$fasta)