kaiju.smk

cluster.json

@@ -3,13 +3,13 @@
 	{
 		"out" : "./.log/out/",
 		"err" : "./.log/err/",
-		"queue" : "maiage.q",
+		"queue" : "short.q,long.q,maiage.q",
 		"cluster" : ""
 	},
 	"kaiju" :
 	{
 		"queue" : "highmem.q,maiage.q",
-		"cluster" : "-l h_vmem={MEM}G"
+		"cluster" : "-l h_vmem=10G"
 	},
 	"khmer" :
 	{

global.smk

@@ -7,6 +7,8 @@ configfile: "./config.json"
 rule all:
 	input:
 		"report/multiqc_report.html",
+		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
 
 include: "../workflow_metagenomics/quality.smk"
 include: "../workflow_metagenomics/preprocess.smk"
+include: "../workflow_metagenomics/kaiju.smk"

kaiju.smk

+def kaiju_input(wildcards):
+	if wildcards.focus == "contigs":
+		return contigs_input(wildcards)
+	elif wildcards.focus == "genes":
+		return ffn_input(wildcards)
+	elif wildcards.focus == "reads":
+		return {"R1": "DATA/trim/{wildcards.sample}_R1.fastq.gz".format(wildcards=wildcards), "R2": "DATA/trim/{wildcards.sample}_R2.fastq.gz".format(wildcards=wildcards)}
+
+rule kaiju:
+	input:
+		unpack(kaiju_input)
+	output:
+		"work/kaiju/{focus,[a-z]+}_{sample}.kaijuNR"
+	threads:
+		8
+	params:
+		input = lambda wildcards, input: "-i %s -j %s"%(input.R1, input.R2) if wildcards.focus == "reads" else "-i %s"%input
+	shell:
+		"kaiju "
+		"-t /db/outils/kaiju/nr/nodes.dmp "
+		"-f /db/outils/kaiju/nr/kaiju_db_nr_euk.fmi "
+		"{params.input} "
+		"-o {output} "
+		"-z {threads}"
+
+rule krona:
+	input:
+		"work/kaiju/{sample}.kaijuNR"
+	output:
+		temp("work/kaiju/{sample}.krona")
+	shell:
+		"kaiju2krona "
+		"-t /db/outils/kaiju/nr/nodes.dmp "
+		"-n /db/outils/kaiju/nr/names.dmp "
+		"-i {input} "
+		"-o {output} "
+		"-u"
+
+rule kronaHTML:
+	input:
+		"work/kaiju/{sample}.krona"
+	output:
+		"report/{sample}-krona.html"
+	shell:
+		"ktImportText "
+		"-o {output} "
+		"{input}"
+
+rule kronaNames:
+	input:
+		"work/kaiju/{sample}.kaijuNR"
+	output:
+		"report/{sample}-taxNames.tsv"
+	shell:
+		"addTaxonNames "
+		"-t /db/outils/kaiju/nr/nodes.dmp "
+		"-n /db/outils/kaiju/nr/names.dmp "
+		"-i {input} "
+		"-o {output} "
+		"-r superkingdom,phylum,order,class,family,genus,species"
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