viromeQC

global.smk

@@ -26,6 +26,8 @@ rule all:
 		#add-on
 		expand("work/addon/{sample}.small_contigs.taxNames.tsv", sample=config["SAMPLES"]),
 		#expand("work/addon/catalogue.{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]),
+		#virome
+		"report/viromeQC.txt",
 
 
 include: "../workflow_metagenomics/quality.smk"
@@ -36,3 +38,4 @@ include: "../workflow_metagenomics/annotation.smk"
 include: "../workflow_metagenomics/count.smk"
 include: "../workflow_metagenomics/catalogue.smk"
 include: "../workflow_metagenomics/add-on.smk"
+include: "../workflow_metagenomics/virome.smk"

virome.smk

+rule viromeQC:
+	input:
+		expand("DATA/trim/{sample}_{R}.fastq.gz", sample=config["SAMPLES"], R=["R1", "R2"])
+	output:
+		"report/viromeQC.txt"
+	threads:
+		8
+	shell:
+		"conda activate viromeQC-1.0 "
+		"&& "
+		"viromeQC.py "
+		"--input {input} "
+		"--output {output} "
+		"--bowtie2_threads {threads} "
+		"--diamond_threads {threads} "
+		"--enrichment_preset environmental "
+		"--tempdir /projet/tmp/ "
+		"&& "
+		"conda deactivate"