diff --git a/.gitignore b/.gitignore index efb05a61..38078fd1 100644 --- a/.gitignore +++ b/.gitignore @@ -9,7 +9,7 @@ assets/genomes assets/mlst_db/blast assets/mlst_db/pubmlst assets/amrfinder_db -assets/wgmlst +assets/wgmlst/*/alleles* assets/prodigal_training_files/* assets/krakenstd work/ diff --git a/README.md b/README.md index c8ee1afa..09be3d56 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ JASEN has been developed for a small set of microbiota (primarily MRSA), but wil ### Copy code locally ``` -git clone --recurse-submodules --single-branch --branch master https://github.com/genomic-medicine-sweden/JASEN.git && cd JASEN +git clone --recurse-submodules --single-branch --branch master git@github.com:genomic-medicine-sweden/JASEN.git && cd JASEN ``` ### Access to OCI registries (Optional) diff --git a/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed b/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed new file mode 100644 index 00000000..c4273e8e --- /dev/null +++ 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b/bin/pipeline_result_processor/prp/parse/phenotype.py index 6a0e7378..28ab5c9e 100644 --- a/bin/pipeline_result_processor/prp/parse/phenotype.py +++ b/bin/pipeline_result_processor/prp/parse/phenotype.py @@ -70,7 +70,7 @@ def _parse_resfinder_amr_genes( coverage=info["coverage"], ref_start_pos=info["ref_start_pos"], ref_end_pos=info["ref_end_pos"], - ref_gene_length=info["ref_seq_lenght"], + ref_gene_length=info["ref_seq_length"], alignment_length=info["alignment_length"], phenotypes=info["phenotypes"], ref_database=info["ref_database"][0], diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config index b98c8423..e006f627 100644 --- a/configs/nextflow.base.config +++ b/configs/nextflow.base.config @@ -38,9 +38,9 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/NC_000913.3.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles" + params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed" - params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/Escherichia_coli.trn" + params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST/Escherichia_coli.trn" params.useVirulenceDbs = ['virulence_ecoli'] } diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config index 662655eb..b4e4b373 100644 --- a/configs/nextflow.hopper.config +++ b/configs/nextflow.hopper.config @@ -49,9 +49,9 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/NC_000913.3.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles" + params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed" - params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/Escherichia_coli.trn" + params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST/Escherichia_coli.trn" params.useVirulenceDbs = ['virulence_ecoli'] } diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config index 7bc81103..820bf573 100644 --- a/configs/nextflow.ngp.config +++ b/configs/nextflow.ngp.config @@ -40,9 +40,9 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/NC_000913.3.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles" + params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed" - params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/Escherichia_coli.trn" + params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST/Escherichia_coli.trn" params.useVirulenceDbs = ['virulence_ecoli'] } diff --git a/configs/nextflow.selftest.config b/configs/nextflow.selftest.config index 8dfbe76e..6dba593a 100644 --- a/configs/nextflow.selftest.config +++ b/configs/nextflow.selftest.config @@ -42,9 +42,9 @@ profiles { // params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed" // params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/NC_000913.3.bed" // params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn" - params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles" + params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST" params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/NC_000913.3.bed" - params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/Escherichia_coli.trn" + params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST/Escherichia_coli.trn" params.useVirulenceDbs = ['virulence_ecoli'] }