From 160964e91b7c7442d30fd46492fa79856a2401cc Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Thu, 19 Sep 2024 19:08:14 +0200 Subject: [PATCH] Add streptococcus profiles --- configs/nextflow.base.config | 24 ++++++++++++++++++++++++ configs/nextflow.ci.config | 28 ++++++++++++++++++++++++++-- configs/nextflow.dev.config | 24 ++++++++++++++++++++++++ configs/nextflow.hopper.config | 24 ++++++++++++++++++++++++ configs/nextflow.ngp.config | 24 ++++++++++++++++++++++++ 5 files changed, 122 insertions(+), 2 deletions(-) diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config index 47934a6..30646e4 100644 --- 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 = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn" + params.useVirulenceDbs = [] + params.useSerotypeDbs = [] + } } singularity { diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config index f5722c5..c63daf7 100644 --- a/configs/nextflow.ci.config +++ b/configs/nextflow.ci.config @@ -21,11 +21,11 @@ params { vcfDir = "vcf" cronCopy = false useKraken = false - useSkesa = false // To use spades set useSkesa = false + useSkesa = true // To use spades set useSkesa = false } dag { - overwrite = true + overwrite = true } profiles { @@ -89,6 +89,30 @@ profiles { params.tbdbBed = "${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 index 375a9ec..836650e 100644 --- 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 = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed/Streptococcus.trn" + params.useVirulenceDbs = [] + params.useSerotypeDbs = [] + } } process { diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config index bdf8525..bd0d598 100644 --- a/configs/nextflow.hopper.config +++ b/configs/nextflow.hopper.config @@ -101,6 +101,30 @@ profiles { params.tbdbBed = "${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 index a566ceb..4c87f26 100644 --- 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 {