viromeQC

global.smk

@@ -27,7 +27,7 @@ rule all:
 		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",
+		expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
 
 
 include: "../workflow_metagenomics/quality.smk"

virome.smk

 rule viromeQC:
 	input:
-		expand("DATA/trim/{sample}_{R}.fastq.gz", sample=config["SAMPLES"], R=["R1", "R2"])
+		R1 = "DATA/trim/{sample}_R1.fastq.gz",
+		R2 = "DATA/trim/{sample}_R2.fastq.gz"
 	output:
-		"report/viromeQC.txt"
+		"report/viromeQC-{sample}.txt"
 	threads:
 		8
 	shell:
 		"conda activate viromeQC-1.0 "
 		"&& "
 		"viromeQC.py "
-		"--input {input} "
+		"--input {input.R1} {input.R2} "
 		"--output {output} "
 		"--bowtie2_threads {threads} "
 		"--diamond_threads {threads} "
 		"--enrichment_preset environmental "
+		"--sample_name {wildcards.sample} "
 		"--tempdir /projet/tmp/ "
 		"&& "
 		"conda deactivate "