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Cedric Midoux
deepomics16S
Commits
001a026d
Commit
001a026d
authored
Aug 01, 2019
by
Cedric Midoux
Browse files
dico for primers
parent
34a3025c
Changes
2
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config.json
View file @
001a026d
{
"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"
}
preprocess.smk
View file @
001a026d
...
...
@@ -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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