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

viromeQC

parent b88960f0
...@@ -27,7 +27,7 @@ rule all: ...@@ -27,7 +27,7 @@ rule all:
expand("work/addon/{sample}.small_contigs.taxNames.tsv", sample=config["SAMPLES"]), expand("work/addon/{sample}.small_contigs.taxNames.tsv", sample=config["SAMPLES"]),
#expand("work/addon/catalogue.{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]), #expand("work/addon/catalogue.{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]),
#virome #virome
"report/viromeQC.txt", expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
include: "../workflow_metagenomics/quality.smk" include: "../workflow_metagenomics/quality.smk"
......
rule viromeQC: rule viromeQC:
input: 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: output:
"report/viromeQC.txt" "report/viromeQC-{sample}.txt"
threads: threads:
8 8
shell: shell:
"conda activate viromeQC-1.0 " "conda activate viromeQC-1.0 "
"&& " "&& "
"viromeQC.py " "viromeQC.py "
"--input {input} " "--input {input.R1} {input.R2} "
"--output {output} " "--output {output} "
"--bowtie2_threads {threads} " "--bowtie2_threads {threads} "
"--diamond_threads {threads} " "--diamond_threads {threads} "
"--enrichment_preset environmental " "--enrichment_preset environmental "
"--sample_name {wildcards.sample} "
"--tempdir /projet/tmp/ " "--tempdir /projet/tmp/ "
"&& " "&& "
"conda deactivate " "conda deactivate "
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