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Commit 328a5fe5 authored by Valentina Galata's avatar Valentina Galata
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taxonomy: kraken: rm not used params, add SR params

parent 25a35203
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......@@ -18,15 +18,13 @@ rule tax_kraken2_contigs:
db="|".join(config["kraken2"]["db"].keys())
threads:
config["kraken2"]["threads"]
params:
params=config["kraken2"]["class"]["contigs"]
conda:
"../envs/kraken2.yaml"
message:
"Tax. classification w/ Kraken2 ({wildcards.db}, contigs)"
shell:
"(date && "
"kraken2 --db {input.db} --threads {threads} --use-names {params.params} --report {output.report} --output {output.labels} {input.contigs} && "
"kraken2 --db {input.db} --threads {threads} --use-names --report {output.report} --output {output.labels} {input.contigs} && "
"date) &> {log}"
rule tax_kraken2_sr:
......@@ -45,7 +43,7 @@ rule tax_kraken2_sr:
threads:
config["kraken2"]["threads"]
params:
params=config["kraken2"]["class"]["sr"]
params="--gzip-compressed --paired"
conda:
"../envs/kraken2.yaml"
message:
......@@ -70,15 +68,13 @@ rule tax_kraken2_lr:
db="|".join(config["kraken2"]["db"].keys())
threads:
config["kraken2"]["threads"]
params:
params=config["kraken2"]["class"]["contigs"]
conda:
"../envs/kraken2.yaml"
message:
"Tax. classification w/ Kraken2 ({wildcards.db}, LR)"
shell:
"(date && "
"kraken2 --db {input.db} --threads {threads} --use-names {params.params} --report {output.report} --output {output.labels} {input.lr} && "
"kraken2 --db {input.db} --threads {threads} --use-names --report {output.report} --output {output.labels} {input.lr} && "
"date) &> {log}"
##################################################
......
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