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Cedric Midoux
workflow_metagenomics
Commits
7e772f24
Commit
7e772f24
authored
Jun 21, 2021
by
Cedric Midoux
Browse files
vibrant
parent
5a8bb8f9
Changes
3
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cluster.json
View file @
7e772f24
...
...
@@ -35,5 +35,10 @@
{
"queue"
:
"highmem.q,maiage.q"
,
"cluster"
:
"-l big_mem"
},
"quast"
:
{
"queue"
:
"highmem.q,maiage.q"
,
"cluster"
:
""
}
}
global.smk
View file @
7e772f24
...
...
@@ -29,6 +29,7 @@ rule all:
expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
expand("work/virhostmatcher/{sample}/done", 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"
...
...
virome.smk
View file @
7e772f24
...
...
@@ -73,3 +73,23 @@ rule crispr:
"-max_target_seqs 1000 "
"&& "
"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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