Add streptococcus profiles

genomic-medicine-sweden · Sep 19, 2024 · 160964e · 160964e
1 parent ceadaf6
commit 160964e
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Showing 5 changed files with 122 additions and 2 deletions.
diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -85,6 +85,30 @@ profiles {
 		params.tbdbBed = "${params.root}/assets/tbprofiler_dbs/bed/converged_who_fohm_tbdb.bed.gz"
 		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
 	}
+
+	streptococcus_pyogenes {
+		params.species = 'streptococcus pyogenes'
+		params.speciesDir = 'spyogenes'
+		params.mlstScheme = 'spyogenes'
+		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
+		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
+		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
+		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
+		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
+
+	streptococcus {
+		params.species = 'streptococcus'
+		params.speciesDir = 'streptococcus'
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
 }
 
 singularity {

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -21,11 +21,11 @@ params {
 	vcfDir = "vcf"
 	cronCopy = false
 	useKraken = false
-	useSkesa = false // To use spades set useSkesa = false
+	useSkesa = true // To use spades set useSkesa = false
 }
 
 dag {
-        overwrite = true
+    overwrite = true
 }
 
 profiles {
@@ -89,6 +89,30 @@ profiles {
 		params.tbdbBed = "${params.root}/assets/tbprofiler_dbs/bed/converged_who_fohm_tbdb.bed.gz"
 		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
 	}
+
+	streptococcus_pyogenes {
+		params.species = 'streptococcus pyogenes'
+		params.speciesDir = 'spyogenes'
+		params.mlstScheme = 'spyogenes'
+		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
+		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
+		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
+		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
+		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
+
+	streptococcus {
+		params.species = 'streptococcus'
+		params.speciesDir = 'streptococcus'
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
 }
 
 process {

diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
@@ -102,6 +102,30 @@ profiles {
 		params.tbdbBed = "${params.root}/assets/tbprofiler_dbs/bed/converged_who_fohm_tbdb.bed.gz"
 		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
 	}
+
+	streptococcus_pyogenes {
+		params.species = 'streptococcus pyogenes'
+		params.speciesDir = 'spyogenes'
+		params.mlstScheme = 'spyogenes'
+		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
+		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
+		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
+		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
+		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
+
+	streptococcus {
+		params.species = 'streptococcus'
+		params.speciesDir = 'streptococcus'
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
 }
 
 process {

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -101,6 +101,30 @@ profiles {
 		params.tbdbBed = "${params.root}/assets/tbprofiler_dbs/bed/converged_who_fohm_tbdb.bed.gz"
 		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
 	}
+
+	streptococcus_pyogenes {
+		params.species = 'streptococcus pyogenes'
+		params.speciesDir = 'spyogenes'
+		params.mlstScheme = 'spyogenes'
+		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
+		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
+		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
+		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
+		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
+
+	streptococcus {
+		params.species = 'streptococcus'
+		params.speciesDir = 'streptococcus'
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
 }
 
 process {

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -111,6 +111,30 @@ profiles {
 		params.tbdbBed = "${params.root}/assets/tbprofiler_dbs/bed/converged_who_fohm_tbdb.bed.gz"
 		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
 	}
+
+	streptococcus_pyogenes {
+		params.species = 'streptococcus pyogenes'
+		params.speciesDir = 'spyogenes'
+		params.mlstScheme = 'spyogenes'
+		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
+		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
+		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
+		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
+		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
+
+	streptococcus {
+		params.species = 'streptococcus'
+		params.speciesDir = 'streptococcus'
+		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
+		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn"
+		params.useVirulenceDbs = []
+		params.useSerotypeDbs = []
+	}
 }
 
 process {