Commit 7e772f24 authored by Cedric Midoux's avatar Cedric Midoux
Browse files

vibrant

parent 5a8bb8f9
...@@ -35,5 +35,10 @@ ...@@ -35,5 +35,10 @@
{ {
"queue" : "highmem.q,maiage.q", "queue" : "highmem.q,maiage.q",
"cluster" : "-l big_mem" "cluster" : "-l big_mem"
},
"quast" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : ""
} }
} }
...@@ -29,6 +29,7 @@ rule all: ...@@ -29,6 +29,7 @@ rule all:
expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]), expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
expand("work/virhostmatcher/{sample}/done", sample=config["SAMPLES"]), expand("work/virhostmatcher/{sample}/done", sample=config["SAMPLES"]),
expand("work/blast/spacer_{sample}.tsv", sample=config["SAMPLES"]), expand("work/blast/spacer_{sample}.tsv", sample=config["SAMPLES"]),
expand("work/vibrant/VIBRANT_{sample}.contigs/VIBRANT_log_run_{sample}.contigs.log", sample=config["SAMPLES"]),
include: "../workflow_metagenomics/quality.smk" include: "../workflow_metagenomics/quality.smk"
......
...@@ -73,3 +73,23 @@ rule crispr: ...@@ -73,3 +73,23 @@ rule crispr:
"-max_target_seqs 1000 " "-max_target_seqs 1000 "
"&& " "&& "
"conda deactivate " "conda deactivate "
rule vibrant:
input:
unpack(contigs_input)
output:
log = "work/vibrant/VIBRANT_{sample}.contigs/VIBRANT_log_run_{sample}.contigs.log"
params:
output = "work/vibrant"
threads:
8
shell:
"conda activate vibrant-1.2.1 "
"&& "
"VIBRANT_run.py "
"-i {input} "
"-f nucl "
"-folder {params.output} "
"-t {threads} "
"&& "
"conda deactivate"
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