├── .github └── workflows │ ├── ci.yml │ └── release.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── README.md ├── assets ├── data │ ├── assemblies │ │ ├── isolate1.fasta │ │ ├── isolate2.fasta │ │ ├── isolate3.fasta │ │ ├── isolate4.fasta │ │ ├── isolate5.fasta │ │ └── ref.fasta │ ├── reads │ │ ├── isolate1_1.fastq.gz │ │ ├── isolate1_2.fastq.gz │ │ ├── isolate2_1.fastq.gz │ │ ├── isolate2_2.fastq.gz │ │ ├── isolate3_1.fastq.gz │ │ ├── isolate3_2.fastq.gz │ │ ├── isolate4_1.fastq.gz │ │ ├── isolate4_2.fastq.gz │ │ ├── isolate5_1.fastq.gz │ │ └── isolate5_2.fastq.gz │ ├── samplesheet.csv │ ├── samplesheet_reads.csv │ ├── snippyref.fasta │ └── test_schema │ │ ├── .genes_list │ │ ├── .schema_config │ │ ├── isolate1-protein1.fasta │ │ ├── isolate1-protein100.fasta │ │ ├── isolate1-protein102.fasta │ │ ├── isolate1-protein103.fasta │ │ ├── isolate1-protein104.fasta │ │ ├── isolate1-protein105.fasta │ │ ├── isolate1-protein106.fasta │ │ ├── isolate1-protein107.fasta │ │ ├── isolate1-protein108.fasta │ │ ├── isolate1-protein109.fasta │ │ ├── isolate1-protein11.fasta │ │ ├── isolate1-protein110.fasta │ │ ├── isolate1-protein111.fasta │ │ ├── isolate1-protein112.fasta │ │ ├── isolate1-protein113.fasta │ │ ├── isolate1-protein114.fasta │ │ ├── isolate1-protein115.fasta │ │ ├── isolate1-protein116.fasta │ │ ├── isolate1-protein117.fasta │ │ ├── isolate1-protein118.fasta │ │ ├── isolate1-protein119.fasta │ │ ├── isolate1-protein12.fasta │ │ ├── isolate1-protein120.fasta │ │ ├── isolate1-protein121.fasta │ │ ├── isolate1-protein122.fasta │ │ ├── isolate1-protein123.fasta │ │ ├── isolate1-protein124.fasta │ │ ├── isolate1-protein125.fasta │ │ ├── isolate1-protein126.fasta │ │ ├── isolate1-protein127.fasta │ │ ├── isolate1-protein128.fasta │ │ ├── isolate1-protein129.fasta │ │ ├── isolate1-protein13.fasta │ │ ├── isolate1-protein130.fasta │ │ ├── isolate1-protein131.fasta │ │ ├── isolate1-protein132.fasta │ │ ├── isolate1-protein133.fasta │ │ ├── isolate1-protein134.fasta │ │ ├── isolate1-protein135.fasta │ │ ├── isolate1-protein136.fasta │ │ ├── isolate1-protein137.fasta │ │ ├── isolate1-protein138.fasta │ │ ├── isolate1-protein139.fasta │ │ ├── isolate1-protein14.fasta │ │ ├── isolate1-protein140.fasta │ │ ├── isolate1-protein141.fasta │ │ ├── isolate1-protein142.fasta │ │ ├── isolate1-protein143.fasta │ │ ├── isolate1-protein15.fasta │ │ ├── isolate1-protein16.fasta │ │ ├── isolate1-protein17.fasta │ │ ├── isolate1-protein18.fasta │ │ ├── isolate1-protein19.fasta │ │ ├── isolate1-protein2.fasta │ │ ├── isolate1-protein20.fasta │ │ ├── isolate1-protein21.fasta │ │ ├── isolate1-protein22.fasta │ │ ├── isolate1-protein23.fasta │ │ ├── isolate1-protein24.fasta │ │ ├── isolate1-protein25.fasta │ │ ├── isolate1-protein26.fasta │ │ ├── isolate1-protein27.fasta │ │ ├── isolate1-protein28.fasta │ │ ├── isolate1-protein29.fasta │ │ ├── isolate1-protein30.fasta │ │ ├── isolate1-protein31.fasta │ │ ├── isolate1-protein32.fasta │ │ ├── isolate1-protein33.fasta │ │ ├── isolate1-protein34.fasta │ │ ├── isolate1-protein35.fasta │ │ ├── isolate1-protein36.fasta │ │ ├── isolate1-protein37.fasta │ │ ├── isolate1-protein39.fasta │ │ ├── isolate1-protein40.fasta │ │ ├── isolate1-protein41.fasta │ │ ├── isolate1-protein42.fasta │ │ ├── isolate1-protein43.fasta │ │ ├── isolate1-protein44.fasta │ │ ├── isolate1-protein45.fasta │ │ ├── isolate1-protein46.fasta │ │ ├── isolate1-protein47.fasta │ │ ├── isolate1-protein48.fasta │ │ ├── isolate1-protein49.fasta │ │ ├── isolate1-protein50.fasta │ │ ├── isolate1-protein51.fasta │ │ ├── isolate1-protein52.fasta │ │ ├── isolate1-protein53.fasta │ │ ├── isolate1-protein54.fasta │ │ ├── isolate1-protein55.fasta │ │ ├── isolate1-protein56.fasta │ │ ├── isolate1-protein57.fasta │ │ ├── isolate1-protein58.fasta │ │ ├── isolate1-protein59.fasta │ │ ├── isolate1-protein60.fasta │ │ ├── isolate1-protein61.fasta │ │ ├── isolate1-protein62.fasta │ │ ├── isolate1-protein63.fasta │ │ ├── isolate1-protein64.fasta │ │ ├── isolate1-protein65.fasta │ │ ├── isolate1-protein66.fasta │ │ ├── isolate1-protein67.fasta │ │ ├── isolate1-protein68.fasta │ │ ├── isolate1-protein69.fasta │ │ ├── isolate1-protein70.fasta │ │ ├── isolate1-protein71.fasta │ │ ├── isolate1-protein72.fasta │ │ ├── isolate1-protein73.fasta │ │ ├── isolate1-protein74.fasta │ │ ├── isolate1-protein75.fasta │ │ ├── isolate1-protein76.fasta │ │ ├── isolate1-protein77.fasta │ │ ├── isolate1-protein78.fasta │ │ ├── isolate1-protein79.fasta │ │ ├── isolate1-protein8.fasta │ │ ├── isolate1-protein80.fasta │ │ ├── isolate1-protein82.fasta │ │ ├── isolate1-protein83.fasta │ │ ├── isolate1-protein84.fasta │ │ ├── isolate1-protein85.fasta │ │ ├── isolate1-protein86.fasta │ │ ├── isolate1-protein87.fasta │ │ ├── isolate1-protein88.fasta │ │ ├── isolate1-protein89.fasta │ │ ├── isolate1-protein9.fasta │ │ ├── isolate1-protein90.fasta │ │ ├── isolate1-protein91.fasta │ │ ├── isolate1-protein92.fasta │ │ ├── isolate1-protein93.fasta │ │ ├── isolate1-protein94.fasta │ │ ├── isolate1-protein95.fasta │ │ ├── isolate1-protein96.fasta │ │ ├── isolate1-protein97.fasta │ │ ├── isolate1-protein98.fasta │ │ ├── isolate1-protein99.fasta │ │ ├── isolate2-protein10.fasta │ │ ├── isolate2-protein7.fasta │ │ ├── isolate3-protein37.fasta │ │ ├── isolate3-protein5.fasta │ │ ├── isolate4-protein3.fasta │ │ ├── isolate4-protein99.fasta │ │ ├── loci_modes │ │ ├── pre_computed │ │ ├── DNAtable1 │ │ └── PROTEINtable1 │ │ ├── short │ │ ├── isolate1-protein100_short.fasta │ │ ├── isolate1-protein102_short.fasta │ │ ├── isolate1-protein103_short.fasta │ │ ├── isolate1-protein104_short.fasta │ │ ├── isolate1-protein105_short.fasta │ │ ├── isolate1-protein106_short.fasta │ │ ├── isolate1-protein107_short.fasta │ │ ├── isolate1-protein108_short.fasta │ │ ├── isolate1-protein109_short.fasta │ │ ├── isolate1-protein110_short.fasta │ │ ├── isolate1-protein111_short.fasta │ │ ├── isolate1-protein112_short.fasta │ │ ├── isolate1-protein113_short.fasta │ │ ├── isolate1-protein114_short.fasta │ │ ├── isolate1-protein115_short.fasta │ │ ├── isolate1-protein116_short.fasta │ │ ├── isolate1-protein117_short.fasta │ │ ├── isolate1-protein118_short.fasta │ │ ├── isolate1-protein119_short.fasta │ │ ├── isolate1-protein11_short.fasta │ │ ├── isolate1-protein120_short.fasta │ │ ├── isolate1-protein121_short.fasta │ │ ├── isolate1-protein122_short.fasta │ │ ├── isolate1-protein123_short.fasta │ │ ├── isolate1-protein124_short.fasta │ │ ├── isolate1-protein125_short.fasta │ │ ├── isolate1-protein126_short.fasta │ │ ├── isolate1-protein127_short.fasta │ │ ├── isolate1-protein128_short.fasta │ │ ├── isolate1-protein129_short.fasta │ │ ├── isolate1-protein12_short.fasta │ │ ├── isolate1-protein130_short.fasta │ │ ├── isolate1-protein131_short.fasta │ │ ├── isolate1-protein132_short.fasta │ │ ├── isolate1-protein133_short.fasta │ │ ├── isolate1-protein134_short.fasta │ │ ├── isolate1-protein135_short.fasta │ │ ├── isolate1-protein136_short.fasta │ │ ├── isolate1-protein137_short.fasta │ │ ├── isolate1-protein138_short.fasta │ │ ├── isolate1-protein139_short.fasta │ │ ├── isolate1-protein13_short.fasta │ │ ├── isolate1-protein140_short.fasta │ │ ├── isolate1-protein141_short.fasta │ │ ├── isolate1-protein142_short.fasta │ │ ├── isolate1-protein143_short.fasta │ │ ├── isolate1-protein14_short.fasta │ │ ├── isolate1-protein15_short.fasta │ │ ├── isolate1-protein16_short.fasta │ │ ├── isolate1-protein17_short.fasta │ │ ├── isolate1-protein18_short.fasta │ │ ├── isolate1-protein19_short.fasta │ │ ├── isolate1-protein1_short.fasta │ │ ├── isolate1-protein20_short.fasta │ │ ├── isolate1-protein21_short.fasta │ │ ├── isolate1-protein22_short.fasta │ │ ├── isolate1-protein23_short.fasta │ │ ├── isolate1-protein24_short.fasta │ │ ├── isolate1-protein25_short.fasta │ │ ├── isolate1-protein26_short.fasta │ │ ├── isolate1-protein27_short.fasta │ │ ├── isolate1-protein28_short.fasta │ │ ├── isolate1-protein29_short.fasta │ │ ├── isolate1-protein2_short.fasta │ │ ├── isolate1-protein30_short.fasta │ │ ├── isolate1-protein31_short.fasta │ │ ├── isolate1-protein32_short.fasta │ │ ├── isolate1-protein33_short.fasta │ │ ├── isolate1-protein34_short.fasta │ │ ├── isolate1-protein35_short.fasta │ │ ├── isolate1-protein36_short.fasta │ │ ├── isolate1-protein37_short.fasta │ │ ├── isolate1-protein39_short.fasta │ │ ├── isolate1-protein40_short.fasta │ │ ├── isolate1-protein41_short.fasta │ │ ├── isolate1-protein42_short.fasta │ │ ├── isolate1-protein43_short.fasta │ │ ├── isolate1-protein44_short.fasta │ │ ├── isolate1-protein45_short.fasta │ │ ├── isolate1-protein46_short.fasta │ │ ├── isolate1-protein47_short.fasta │ │ ├── isolate1-protein48_short.fasta │ │ ├── isolate1-protein49_short.fasta │ │ ├── isolate1-protein50_short.fasta │ │ ├── isolate1-protein51_short.fasta │ │ ├── isolate1-protein52_short.fasta │ │ ├── isolate1-protein53_short.fasta │ │ ├── isolate1-protein54_short.fasta │ │ ├── isolate1-protein55_short.fasta │ │ ├── isolate1-protein56_short.fasta │ │ ├── isolate1-protein57_short.fasta │ │ ├── isolate1-protein58_short.fasta │ │ ├── isolate1-protein59_short.fasta │ │ ├── isolate1-protein60_short.fasta │ │ ├── isolate1-protein61_short.fasta │ │ ├── isolate1-protein62_short.fasta │ │ ├── isolate1-protein63_short.fasta │ │ ├── isolate1-protein64_short.fasta │ │ ├── isolate1-protein65_short.fasta │ │ ├── isolate1-protein66_short.fasta │ │ ├── isolate1-protein67_short.fasta │ │ ├── isolate1-protein68_short.fasta │ │ ├── isolate1-protein69_short.fasta │ │ ├── isolate1-protein70_short.fasta │ │ ├── isolate1-protein71_short.fasta │ │ ├── isolate1-protein72_short.fasta │ │ ├── isolate1-protein73_short.fasta │ │ ├── isolate1-protein74_short.fasta │ │ ├── isolate1-protein75_short.fasta │ │ ├── isolate1-protein76_short.fasta │ │ ├── isolate1-protein77_short.fasta │ │ ├── isolate1-protein78_short.fasta │ │ ├── isolate1-protein79_short.fasta │ │ ├── isolate1-protein80_short.fasta │ │ ├── isolate1-protein82_short.fasta │ │ ├── isolate1-protein83_short.fasta │ │ ├── isolate1-protein84_short.fasta │ │ ├── isolate1-protein85_short.fasta │ │ ├── isolate1-protein86_short.fasta │ │ ├── isolate1-protein87_short.fasta │ │ ├── isolate1-protein88_short.fasta │ │ ├── isolate1-protein89_short.fasta │ │ ├── isolate1-protein8_short.fasta │ │ ├── isolate1-protein90_short.fasta │ │ ├── isolate1-protein91_short.fasta │ │ ├── isolate1-protein92_short.fasta │ │ ├── isolate1-protein93_short.fasta │ │ ├── isolate1-protein94_short.fasta │ │ ├── isolate1-protein95_short.fasta │ │ ├── isolate1-protein96_short.fasta │ │ ├── isolate1-protein97_short.fasta │ │ ├── isolate1-protein98_short.fasta │ │ ├── isolate1-protein99_short.fasta │ │ ├── isolate1-protein9_short.fasta │ │ ├── isolate2-protein10_short.fasta │ │ ├── isolate2-protein7_short.fasta │ │ ├── isolate3-protein37_short.fasta │ │ ├── isolate3-protein5_short.fasta │ │ ├── isolate4-protein3_short.fasta │ │ ├── isolate4-protein99_short.fasta │ │ └── self_scores │ │ └── test_training_file.trn ├── env.yml ├── r_docker_buildfile └── r_env.yml ├── bin ├── ani_report.Rmd ├── calculate_distances.R ├── cgmlst_report.Rmd ├── core_gene_report.Rmd ├── core_genome_report.Rmd ├── filter_cgmlst_data.R ├── gen_report.R ├── generate_input.R ├── mapping_report.Rmd └── snippyfy.bash ├── conf ├── base.config ├── hpc.config ├── modules.config ├── test_ani.config ├── test_cgmlst.config ├── test_core_gene.config ├── test_core_genome.config └── test_mapping.config ├── examples ├── core_gene_report.html ├── core_genome_report.html └── mapping_report.html ├── logo.png ├── main.nf ├── modules ├── BAKTA.nf ├── CHEWBBACA.nf ├── FASTANI.nf ├── GUBBINS.nf ├── IQTREE.nf ├── MASKRC.nf ├── MLST.nf ├── PANAROO.nf ├── PARSNP.nf ├── PREPARE_TABLE.nf ├── REPORT.nf ├── RSCRIPTS.nf ├── SEQKIT.nf ├── SNIPPY.nf ├── SNPDIST.nf └── SNPSITES.nf ├── 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