Commit 9dfbb487 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

DADA2 filterAndTrim

parent 3299174d
library(dada2)
filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
......@@ -15,3 +15,11 @@ rule cutadapt:
"--match-read-wildcards "
"-o {output} "
"{input} "
rule filter:
input:
"work/cutadapt/{sample}.fastq.gz"
output:
"work/filter/{sample}.fastq.gz"
script:
"filterAndTrim.R"
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