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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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Cedric Midoux
deepomics16S
Commits
3299174d
Commit
3299174d
authored
Apr 04, 2019
by
Cedric Midoux
Browse files
cutadapt
parent
4cfc3cee
Changes
3
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config.json
View file @
3299174d
{
"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"
}
global.smk
View file @
3299174d
...
...
@@ -8,3 +8,4 @@ rule all:
"report/multiqc_report.html"
include: "quality.smk"
include: "preprocess.smk"
preprocess.smk
0 → 100644
View file @
3299174d
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} "
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