Commit 001a026d authored by Midoux Cedric's avatar Midoux Cedric
Browse files

dico for primers

parent 34a3025c
{
"THREADS": 8,
"MEM": 10,
"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"],
"FIVE_PRIMER": "GTGYCAGCMGCCGCGGTA",
"THREE_PRIMER": "ACTYAAAKGAATTGRCGGGG",
"FIVE_PRIMER": {"4A": "GTGYCAGCMGCCGCGGTA", "5A": "GTGYCAGCMGCCGCGGTA","6A": "GTGYCAGCMGCCGCGGTA","7A": "GTGYCAGCMGCCGCGGTA","8A": "GTGYCAGCMGCCGCGGTA","9A": "GTGYCAGCMGCCGCGGTA","10A": "GTGYCAGCMGCCGCGGTA","11A": "GTGYCAGCMGCCGCGGTA","12A": "GTGYCAGCMGCCGCGGTA"},
"THREE_PRIMER": {"4A": "ACTYAAAKGAATTGRCGGGG", "5A": "ACTYAAAKGAATTGRCGGGG","6A": "ACTYAAAKGAATTGRCGGGG","7A": "ACTYAAAKGAATTGRCGGGG","8A": "ACTYAAAKGAATTGRCGGGG","9A": "ACTYAAAKGAATTGRCGGGG","10A": "ACTYAAAKGAATTGRCGGGG","11A": "ACTYAAAKGAATTGRCGGGG","12A": "ACTYAAAKGAATTGRCGGGG"},
"DATABASE": "/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
}
......@@ -4,8 +4,8 @@ rule cutadapt:
output:
"work/cutadapt/{sample}.fastq.gz"
params:
five = config["FIVE_PRIMER"],
three = config["THREE_PRIMER"]
five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
shell:
"cutadapt "
"-g {params.five} "
......
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