Commit 46c66daf authored by Midoux Cedric's avatar Midoux Cedric
Browse files

FROGS affiliation

parent 01fe044d
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}"
......@@ -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"
}
......@@ -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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