Commit d48141a8 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

viromeQC

parent 1ab91ebc
...@@ -26,6 +26,8 @@ rule all: ...@@ -26,6 +26,8 @@ rule all:
#add-on #add-on
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
"report/viromeQC.txt",
include: "../workflow_metagenomics/quality.smk" include: "../workflow_metagenomics/quality.smk"
...@@ -36,3 +38,4 @@ include: "../workflow_metagenomics/annotation.smk" ...@@ -36,3 +38,4 @@ include: "../workflow_metagenomics/annotation.smk"
include: "../workflow_metagenomics/count.smk" include: "../workflow_metagenomics/count.smk"
include: "../workflow_metagenomics/catalogue.smk" include: "../workflow_metagenomics/catalogue.smk"
include: "../workflow_metagenomics/add-on.smk" include: "../workflow_metagenomics/add-on.smk"
include: "../workflow_metagenomics/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"
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