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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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Cedric Midoux
deepomics16S
Commits
46c66daf
Commit
46c66daf
authored
Apr 11, 2019
by
Cedric Midoux
Browse files
FROGS affiliation
parent
01fe044d
Changes
3
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affiliation.smk
0 → 100644
View file @
46c66daf
rule affiliation:
input:
biom = "work/dada/dada.biom",
fasta = "work/dada/seqtab.fasta"
output:
html = "work/FROGS/affiliation.html",
biom = "work/FROGS/affiliation.biom"
threads:
config["THREADS"]
params:
mem_tot = config["THREADS"]*MEM,
database = config["DATABASE"]
shell:
"affiliation_OTU.py "
"--nb-cpu {threads} "
"--java-mem {params.mem_tot} "
"--reference {params.database} "
"--input-biom {input.biom} "
"--input-fasta {input.fasta} "
"--summary {output.html} "
"--output-biom {output.biom}"
config.json
View file @
46c66daf
...
...
@@ -3,5 +3,6 @@
"MEM"
:
10
,
"SAMPLES"
:
[
"4A"
,
"5A"
,
"6A"
,
"7A"
,
"8A"
,
"9A"
,
"10A"
,
"11A"
,
"12A"
],
"FIVE_PRIMER"
:
"GTGYCAGCMGCCGCGGTA"
,
"THREE_PRIMER"
:
"ACTYAAAKGAATTGRCGGGG"
"THREE_PRIMER"
:
"ACTYAAAKGAATTGRCGGGG"
,
"DATABASE"
:
"/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
}
global.smk
View file @
46c66daf
...
...
@@ -8,8 +8,10 @@ rule all:
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.fasta",
"work/dada/seqtab.tsv"
"work/dada/seqtab.tsv",
"work/FROGS/affiliation.biom"
include: "quality.smk"
include: "preprocess.smk"
include: "dada2.smk"
include: "affiliation.smk"
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