FROGS affiliation

affiliation.smk

+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

@@ -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

@@ -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"