From 9dfbb487e237f8cae3f88c02fccee63833e5ef6c Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Thu, 4 Apr 2019 17:15:00 +0200
Subject: [PATCH] DADA2 filterAndTrim

---
 filterAndTrim.R | 3 +++
 preprocess.smk  | 8 ++++++++
 2 files changed, 11 insertions(+)
 create mode 100644 filterAndTrim.R

diff --git a/filterAndTrim.R b/filterAndTrim.R
new file mode 100644
index 0000000..c1ab729
--- /dev/null
+++ b/filterAndTrim.R
@@ -0,0 +1,3 @@
+library(dada2)
+
+filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
diff --git a/preprocess.smk b/preprocess.smk
index d5f8f3f..56b94b6 100644
--- 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"
-- 
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