DADA2 filterAndTrim

9dfbb487 · Midoux Cedric · 3299174d · 9dfbb487 · 9dfbb487
Commit 9dfbb487 authored 6 years ago by Midoux Cedric
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--- a/filterAndTrim.R
+++ b/filterAndTrim.R
+library(dada2)
+filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
--- a/preprocess.smk
+++ b/preprocess.smk
@@ -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"