From 3b65b798f2a6fc87f8ca02bc4d94ad577f4bf205 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Wed, 13 Nov 2024 15:25:50 +0100 Subject: [PATCH] Mv mlstBlastDb to global in config --- configs/nextflow.base.config | 6 +----- configs/nextflow.ci.config | 6 +----- configs/nextflow.dev.config | 6 +----- configs/nextflow.hopper.config | 6 +----- configs/nextflow.ngp.config | 12 ++++-------- 5 files changed, 8 insertions(+), 28 deletions(-) diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config index 8d518180..07e4df4b 100644 --- a/configs/nextflow.base.config +++ b/configs/nextflow.base.config @@ -5,6 +5,7 @@ params { pointfinderDb = "${root}/assets/pointfinder_db" serotypefinderDb = "${root}/assets/serotypefinder_db" virulencefinderDb = "${root}/assets/virulencefinder_db" + mlstBlastDb = "${root}/assets/mlst_db/blast" pubMlstDb = "${root}/assets/mlst_db/pubmlst" krakenDb = "/filepath/to/kraken_db" //edit if useKraken = true workDir = "/filepath/to/workdir" //edit @@ -32,7 +33,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed/Staphylococcus_aureus.trn" @@ -51,7 +51,6 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed" params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases" @@ -68,7 +67,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn" @@ -99,7 +97,6 @@ profiles { 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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn" @@ -115,7 +112,6 @@ profiles { params.referenceGenome = null params.referenceGenomeIdx = null params.referenceGenomeGff = null - params.mlstBlastDb = null params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed" params.shigapassDb = null params.coreLociBed = null diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config index e9db8eda..f0ec8517 100644 --- a/configs/nextflow.ci.config +++ b/configs/nextflow.ci.config @@ -5,6 +5,7 @@ params { pointfinderDb = "${root}/assets/pointfinder_db" serotypefinderDb = "${root}/assets/serotypefinder_db" virulencefinderDb = "${root}/assets/virulencefinder_db" + mlstBlastDb = "${root}/assets/mlst_db/blast" pubMlstDb = "${root}/assets/mlst_db/pubmlst" krakenDb = "/tmp/jsn" //edit if useKraken = true workDir = "/tmp/jsn" //edit @@ -36,7 +37,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed/Staphylococcus_aureus.trn" @@ -55,7 +55,6 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed" params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases" @@ -72,7 +71,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn" @@ -103,7 +101,6 @@ profiles { 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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn" @@ -119,7 +116,6 @@ profiles { params.referenceGenome = null params.referenceGenomeIdx = null params.referenceGenomeGff = null - params.mlstBlastDb = null params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed" params.shigapassDb = null params.coreLociBed = null diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config index 08c8fa79..46463b36 100644 --- a/configs/nextflow.dev.config +++ b/configs/nextflow.dev.config @@ -8,6 +8,7 @@ params { pointfinderDb = "${root}/assets/pointfinder_db" serotypefinderDb = "${root}/assets/serotypefinder_db" virulencefinderDb = "${root}/assets/virulencefinder_db" + mlstBlastDb = "${root}/assets/mlst_db/blast" pubMlstDb = "${root}/assets/mlst_db/pubmlst" krakenDb = "/fs1/resources/ref/micro/krakenstd" // INPUT & OUTPUT // @@ -45,7 +46,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed/Staphylococcus_aureus.trn" @@ -65,7 +65,6 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed" @@ -83,7 +82,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn" @@ -115,7 +113,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.gff" - params.mlstBlastDb = "${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_000006785.2.bed" params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn" @@ -131,7 +128,6 @@ profiles { params.referenceGenome = null params.referenceGenomeIdx = null params.referenceGenomeGff = null - params.mlstBlastDb = null params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed" params.shigapassDb = null params.coreLociBed = null diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config index b9d7d717..b1ccb459 100644 --- a/configs/nextflow.hopper.config +++ b/configs/nextflow.hopper.config @@ -8,6 +8,7 @@ params { pointfinderDb = "${root}/assets/pointfinder_db" serotypefinderDb = "${root}/assets/serotypefinder_db" virulencefinderDb = "${root}/assets/virulencefinder_db" + mlstBlastDb = "${root}/assets/mlst_db/blast" pubMlstDb = "${root}/assets/mlst_db/pubmlst" krakenDb = "/fs1/resources/ref/micro/krakenstd" // INPUT & OUTPUT // @@ -44,7 +45,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed/Staphylococcus_aureus.trn" @@ -64,7 +64,6 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed" params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases" @@ -82,7 +81,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn" @@ -115,7 +113,6 @@ profiles { 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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn" @@ -131,7 +128,6 @@ profiles { params.referenceGenome = null params.referenceGenomeIdx = null params.referenceGenomeGff = null - params.mlstBlastDb = null params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed" params.shigapassDb = null params.coreLociBed = null diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config index 28911fc9..5fc87289 100644 --- a/configs/nextflow.ngp.config +++ b/configs/nextflow.ngp.config @@ -2,10 +2,11 @@ params { penv = "OpenMP" root = "/gms-apps/pipelines/jasen" //edit amrfinderDb = "${root}/assets/amrfinder_db/latest" - resfinderDb = "${params.root}/assets/resfinder_db" - pointfinderDb = "${params.root}/assets/pointfinder_db" + resfinderDb = "${root}/assets/resfinder_db" + pointfinderDb = "${root}/assets/pointfinder_db" serotypefinderDb = "${root}/assets/serotypefinder_db" - virulencefinderDb = "${params.root}/assets/virulencefinder_db" + virulencefinderDb = "${root}/assets/virulencefinder_db" + mlstBlastDb = "${root}/assets/mlst_db/blast" pubMlstDb = "${root}/assets/mlst_db/pubmlst" krakenDb = "/gms-home/isasyl/code/JASEN" //edit if useKraken = true workDir = "/gms-apps/pipelines/jasen/trash" //edit @@ -58,7 +59,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed" params.trainingFile = "${params.root}/assets/prodigal_training_files/Staphylococcus_aureus.trn" @@ -77,7 +77,6 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed" params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases" @@ -94,7 +93,6 @@ profiles { params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta" params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai" params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff" - params.mlstBlastDb = "${params.root}/assets/mlst_db/blast" params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed" params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed" params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn" @@ -125,7 +123,6 @@ profiles { params.referenceGenome = "${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" @@ -141,7 +138,6 @@ profiles { params.referenceGenome = null params.referenceGenomeIdx = null params.referenceGenomeGff = null - params.mlstBlastDb = null params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed" params.shigapassDb = null params.coreLociBed = null