Commit da4fa296 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

DADA2

parent 9dfbb487
library(dada2)
derep <- derepFastq(snakemake@input[[1]], verbose = TRUE)
err <- learnErrors(snakemake@input[[1]], multithread = snakemake@threads, verbose = TRUE)
dada <- dada(derep, err = err, multithread = snakemake@threads, verbose = TRUE)
saveRDS(dada, snakemake@output[[1]])
rule dada2:
input:
"work/filter/{sample}.fastq.gz"
output:
"work/dada/{sample}.rds"
threads:
config["THREADS"]
script:
"dada2.R"
...@@ -5,7 +5,9 @@ SAMPLES=config["SAMPLES"] ...@@ -5,7 +5,9 @@ SAMPLES=config["SAMPLES"]
rule all: rule all:
input: input:
"report/multiqc_report.html" "report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES)
include: "quality.smk" include: "quality.smk"
include: "preprocess.smk" include: "preprocess.smk"
include: "dada2.smk"
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment