From 328a5fe5b98592923365e9a710d4bf7c64a32794 Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Wed, 14 Oct 2020 13:41:49 +0200
Subject: [PATCH] taxonomy: kraken: rm not used params, add SR params
---
workflow/rules/taxonomy.smk | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/workflow/rules/taxonomy.smk b/workflow/rules/taxonomy.smk
index b21c3d4..bf4fbbc 100644
--- a/workflow/rules/taxonomy.smk
+++ b/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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