vibrant

cluster.json

@@ -35,5 +35,10 @@
 	{
 		"queue" : "highmem.q,maiage.q",
 		"cluster" : "-l big_mem"
+	},
+	"quast" :
+	{
+		"queue" : "highmem.q,maiage.q",
+		"cluster" : ""
 	}
 }

global.smk

@@ -29,6 +29,7 @@ rule all:
 		expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
 		expand("work/virhostmatcher/{sample}/done", sample=config["SAMPLES"]),
 		expand("work/blast/spacer_{sample}.tsv", sample=config["SAMPLES"]),
+		expand("work/vibrant/VIBRANT_{sample}.contigs/VIBRANT_log_run_{sample}.contigs.log", sample=config["SAMPLES"]),
 
 
 include: "../workflow_metagenomics/quality.smk"

virome.smk

@@ -73,3 +73,23 @@ rule crispr:
 		"-max_target_seqs 1000 "
 		"&& "
 		"conda deactivate "
+
+rule vibrant:
+	input:
+		unpack(contigs_input)
+	output:
+		log = "work/vibrant/VIBRANT_{sample}.contigs/VIBRANT_log_run_{sample}.contigs.log"
+	params:
+		output = "work/vibrant"
+	threads:
+		8
+	shell:
+		"conda activate vibrant-1.2.1 "
+		"&& "
+		"VIBRANT_run.py "
+		"-i {input} "
+		"-f nucl "
+		"-folder {params.output} "
+		"-t {threads} "
+		"&& "
+		"conda deactivate"