Commit c9084505 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

DADA2 makeSequenceTable

parent da4fa296
...@@ -7,3 +7,13 @@ rule dada2: ...@@ -7,3 +7,13 @@ rule dada2:
config["THREADS"] config["THREADS"]
script: script:
"dada2.R" "dada2.R"
rule makeSequenceTable:
input:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
"work/dada/seqtab.rds"
threads:
config["THREADS"]
script:
"makeSequenceTable.R"
...@@ -6,7 +6,8 @@ SAMPLES=config["SAMPLES"] ...@@ -6,7 +6,8 @@ SAMPLES=config["SAMPLES"]
rule all: 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"
include: "quality.smk" include: "quality.smk"
include: "preprocess.smk" include: "preprocess.smk"
......
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]])
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