diff --git a/rules/blast.smk b/rules/blast.smk index aba2efa..26177fe 100644 --- a/rules/blast.smk +++ b/rules/blast.smk @@ -14,11 +14,11 @@ rule prepare_taxonomy_data: ## Blast against NT virus database rule blastn_virus: input: - query = rules.parse_megablast.output.unmapped, - db = config["virus_nt"] + query = rules.parse_megablast.output.unmapped output: out = "blast/{sample}_blastn_virus_{n,\d+}.tsv" params: + db = config["virus_nt"], task = "blastn", evalue = config["blastn_virus"]["evalue"], db_soft_mask = config["blastn_virus"]["db_soft_mask"], @@ -46,11 +46,11 @@ rule parse_blastn_virus: ## Blastx unmapped sequences against NR virus database rule blastx_virus: input: - query = rules.parse_blastn_virus.output.unmapped, - db = config["virus_nr"] + query = rules.parse_blastn_virus.output.unmapped output: out = "blast/{sample}_blastx_virus_{n}.tsv" params: + db = config["virus_nr"], word_size = 6, evalue = config["blastx_virus"]["evalue"], db_soft_mask = config["blastx_virus"]["db_soft_mask"], @@ -148,11 +148,11 @@ rule refbac_unmapped_masked: ## MegaBlast against NT to remove host sequences rule megablast_nt: input: - query = rules.refbac_unmapped_masked.output, - db = config["nt"] + query = rules.refbac_unmapped_masked.output output: out = "blast/{sample}_megablast_nt_{n,\d+}.tsv" params: + db = config["nt"], task = "megablast", evalue = config["megablast_nt"]["evalue"], word_size = config["megablast_nt"]["word_size"], @@ -180,11 +180,11 @@ rule parse_megablast_nt: ## Blastn against NT database rule blastn_nt: input: - query = rules.parse_megablast_nt.output.unmapped, - db = config["nt"] + query = rules.parse_megablast_nt.output.unmapped output: out = "blast/{sample}_blastn_nt_{n,\d+}.tsv" params: + db = config["nt"], task = "blastn", evalue = config["blastn_nt"]["evalue"], max_hsps = config["blastn_nt"]["max_hsps"], @@ -211,11 +211,11 @@ rule parse_blastn_nt: ## Blastx unmapped sequences against NR virus database rule blastx_nr: input: - query = rules.parse_blastn_nt.output.unmapped, - db = config["nr"] + query = rules.parse_blastn_nt.output.unmapped output: out = "blast/{sample}_blastx_nr_{n,\d+}.tsv" params: + db = config["nr"], word_size = 6, evalue = config["blastx_nr"]["evalue"], max_hsps = config["blastx_nr"]["max_hsps"], diff --git a/rules/refgenomefilter.smk b/rules/refgenomefilter.smk index 3f09450..8ed1e64 100644 --- a/rules/refgenomefilter.smk +++ b/rules/refgenomefilter.smk @@ -33,11 +33,11 @@ rule refgenome_unmapped_masked: ## MegaBlast against reference genome to remove host sequences rule megablast_refgenome: input: - query = rules.refgenome_unmapped_masked.output, - db = config["ref_genome"] + query = rules.refgenome_unmapped_masked.output output: out = "refgenomefilter/{sample}_megablast_{n}.tsv" params: + db = config["ref_genome"], task = "megablast", perc_identity = config["megablast_ref_genome"]["perc_identity"], evalue = config["megablast_ref_genome"]["evalue"],