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

fasta export

parent c9084505
...@@ -12,7 +12,8 @@ rule makeSequenceTable: ...@@ -12,7 +12,8 @@ rule makeSequenceTable:
input: input:
expand("work/dada/{sample}.rds", sample=SAMPLES) expand("work/dada/{sample}.rds", sample=SAMPLES)
output: output:
"work/dada/seqtab.rds" table = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta"
threads: threads:
config["THREADS"] config["THREADS"]
script: script:
......
...@@ -7,7 +7,8 @@ rule all: ...@@ -7,7 +7,8 @@ rule all:
input: input:
"report/multiqc_report.html", "report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES), expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.rds" "work/dada/seqtab.rds",
"work/dada/seqtab.fasta"
include: "quality.smk" include: "quality.smk"
include: "preprocess.smk" include: "preprocess.smk"
......
...@@ -2,4 +2,5 @@ library(dada2) ...@@ -2,4 +2,5 @@ library(dada2)
seqtab <- makeSequenceTable(lapply(snakemake@input, readRDS), orderBy = "abundance") seqtab <- makeSequenceTable(lapply(snakemake@input, readRDS), orderBy = "abundance")
seqtab.nochim <- removeBimeraDenovo(seqtab, method="consensus", multithread = snakemake@threads, verbose = TRUE) 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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