taxonomy: kraken: rm not used params, add SR params

workflow/rules/taxonomy.smk

@@ -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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