Commit 3299174d authored by Midoux Cedric's avatar Midoux Cedric
Browse files

cutadapt

parent 4cfc3cee
{
"THREADS": 8,
"MEM": 10,
"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"]
"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"],
"FIVE_PRIMER": "GTGYCAGCMGCCGCGGTA",
"THREE_PRIMER": "ACTYAAAKGAATTGRCGGGG"
}
......@@ -8,3 +8,4 @@ rule all:
"report/multiqc_report.html"
include: "quality.smk"
include: "preprocess.smk"
rule cutadapt:
input:
"DATA/{sample}.fastq.gz"
output:
"work/cutadapt/{sample}.fastq.gz"
params:
five = config["FIVE_PRIMER"],
three = config["THREE_PRIMER"]
shell:
"cutadapt "
"-g {params.five} "
"-a {params.three} "
"--error-rate 0.1 "
"--discard-untrimmed "
"--match-read-wildcards "
"-o {output} "
"{input} "
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