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" -- GitLab