Commit 5efe1830 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

viromeQC

parent b88960f0
......@@ -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"
......
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 "
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