Commit 4b986440 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

fasta export

parent c9084505
......@@ -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:
......
......@@ -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"
......
......@@ -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)
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