public_health_bioinformatics/mkdocs.yml at main · theiagen/public_health_bioinformatics · GitHub

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site_name: Public Health Bioinformatics
site_author: Theiagen Genomics
site_description: A collection of bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

site_url: https://theiagen.github.io/public_health_bioinformatics/
edit_uri: "edit/main/docs/"

repo_url: https://github.com/theiagen/public_health_bioinformatics

nav:
  - Public Health Bioinformatics:
      - Home: index.md
      - Getting Started:
          - With the Command-Line: getting_started/commandline.md
          - With Terra.bio: getting_started/terra.md
          - Workflow Failure Philosophy: getting_started/philosophy.md
      - Other Resources:
          - Available SOPs: guides/sops.md
          - All Tools: guides/all_tools.md
          - Database and Docker Versions: guides/versions.md
          - Glossary: guides/glossary.md
      - Guides:
          - Guide to GAMBIT: guides/gambit.md
          - Guide to GAMBIT Database Creation: guides/gambit_database.md
          - Guide to Phylogenetics: guides/phylogenetics.md
          - Guide to Running Custom Organisms on TheiaCoV: guides/custom_organisms.md
      - Workflows:
          - Workflows by Type:
              - Overview Table: workflows_overview/workflows_type.md
              - Data Import:
                  - Assembly_Fetch: workflows/data_import/assembly_fetch.md
                  - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
                  - Create_Terra_Table: workflows/data_import/create_terra_table.md
                  - Fetch_SRR_Accession: workflows/data_import/fetch_srr_accession.md
                  - ONT_Barcode_Concatenation: workflows/data_import/ont_barcode_concatenation.md
                  - SRA_Fetch: workflows/data_import/sra_fetch.md
              - Genomic Characterization:
                  - Freyja Workflow Series: workflows/genomic_characterization/freyja.md
                  - Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
                  - TheiaCoV™ Workflow Series: workflows/genomic_characterization/theiacov.md
                  - TheiaEuk™ Workflow Series: workflows/genomic_characterization/theiaeuk.md
                  - TheiaMeta™: workflows/genomic_characterization/theiameta.md
                  - TheiaProk™ Workflow Series: workflows/genomic_characterization/theiaprok.md
                  - TheiaViral™ Workflow Series: workflows/genomic_characterization/theiaviral.md
                  - VADR_Update: workflows/genomic_characterization/vadr_update.md
              - Phylogenetic Construction:
                  - Augur: workflows/phylogenetic_construction/augur.md
                  - Core_Gene_SNP: workflows/phylogenetic_construction/core_gene_snp.md
                  - Clair3_Variants_ONT: workflows/phylogenetic_construction/clair3_variants.md
                  - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
                  - kSNP3: workflows/phylogenetic_construction/ksnp3.md
                  - kSNP4: workflows/phylogenetic_construction/ksnp4.md
                  - Lyve_SET: workflows/phylogenetic_construction/lyve_set.md
                  - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
                  - Snippy_Streamline: workflows/phylogenetic_construction/snippy_streamline.md
                  - Snippy_Streamline_FASTA: workflows/phylogenetic_construction/snippy_streamline_fasta.md
                  - Snippy_Tree: workflows/phylogenetic_construction/snippy_tree.md
                  - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
              - Phylogenetic Placement:
                  - Nextclade_Batch: workflows/phylogenetic_placement/nextclade_batch.md
                  - Usher: workflows/phylogenetic_placement/usher.md
              - Public Data Sharing:
                  - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md
                  - Terra_2_ENA: workflows/public_data_sharing/terra_2_ena.md
                  - Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md
                  - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
              - Exporting Data from Terra:
                  - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
                  - Transfer_Column_Content: workflows/data_export/transfer_column_content.md
                  - Zip_Column_Content: workflows/data_export/zip_column_content.md
                  - Microreact_Export: workflows/data_export/microreact_export.md
              - Standalone:
                  - AMR_Search: workflows/standalone/amr_search.md
                  - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
                  - Dorado_Basecalling: workflows/standalone/dorado_basecalling.md
                  - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
                  - GAMBIT_Query: workflows/standalone/gambit_query.md
                  - Kraken2: workflows/standalone/kraken2.md
                  - Metabuli: workflows/standalone/metabuli.md
                  - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
                  - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
                  - PhyloCompare: workflows/standalone/phylocompare.md
                  - RASUSA: workflows/standalone/rasusa.md
                  - Rename_FASTQ: workflows/standalone/rename_fastq.md
                  - TBProfiler_tNGS: workflows/standalone/tbprofiler_tngs.md
                  - TheiaValidate™: workflows/standalone/theiavalidate.md
          - Workflows by Kingdom:
              - Overview Table: workflows_overview/workflows_kingdom.md
              - Any Taxa:
                  - AMR_Search: workflows/standalone/amr_search.md
                  - Assembly_Fetch: workflows/data_import/assembly_fetch.md
                  - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
                  - Clair3_Variants_ONT: workflows/phylogenetic_construction/clair3_variants.md
                  - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
                  - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
                  - Create_Terra_Table: workflows/data_import/create_terra_table.md
                  - Dorado_Basecalling: workflows/standalone/dorado_basecalling.md
                  - Fetch_SRR_Accession: workflows/data_import/fetch_srr_accession.md
                  - Kraken2: workflows/standalone/kraken2.md
                  - Metabuli: workflows/standalone/metabuli.md
                  - Microreact_Export: workflows/data_export/microreact_export.md
                  - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
                  - ONT_Barcode_Concatenation: workflows/data_import/ont_barcode_concatenation.md
                  - PhyloCompare: workflows/standalone/phylocompare.md
                  - RASUSA: workflows/standalone/rasusa.md
                  - Rename_FASTQ: workflows/standalone/rename_fastq.md
                  - SRA_Fetch: workflows/data_import/sra_fetch.md
                  - TheiaMeta™: workflows/genomic_characterization/theiameta.md
                  - TheiaValidate™: workflows/standalone/theiavalidate.md
                  - Transfer_Column_Content: workflows/data_export/transfer_column_content.md
                  - Zip_Column_Content: workflows/data_export/zip_column_content.md
              - Bacteria:
                  - Core_Gene_SNP: workflows/phylogenetic_construction/core_gene_snp.md
                  - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
                  - GAMBIT_Query: workflows/standalone/gambit_query.md
                  - kSNP3: workflows/phylogenetic_construction/ksnp3.md
                  - kSNP4: workflows/phylogenetic_construction/ksnp4.md
                  - Lyve_SET: workflows/phylogenetic_construction/lyve_set.md
                  - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
                  - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
                  - Snippy_Streamline: workflows/phylogenetic_construction/snippy_streamline.md
                  - Snippy_Streamline_FASTA: workflows/phylogenetic_construction/snippy_streamline_fasta.md
                  - Snippy_Tree: workflows/phylogenetic_construction/snippy_tree.md
                  - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
                  - TBProfiler_tNGS: workflows/standalone/tbprofiler_tngs.md
                  - Terra_2_ENA: workflows/public_data_sharing/terra_2_ena.md
                  - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
                  - TheiaProk™ Workflow Series: workflows/genomic_characterization/theiaprok.md
              - Mycotics:
                  - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
                  - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
                  - GAMBIT_Query: workflows/standalone/gambit_query.md
                  - kSNP3: workflows/phylogenetic_construction/ksnp3.md
                  - kSNP4: workflows/phylogenetic_construction/ksnp4.md
                  - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
                  - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
                  - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
                  - TheiaEuk™ Workflow Series: workflows/genomic_characterization/theiaeuk.md
              - Viral:
                  - Augur: workflows/phylogenetic_construction/augur.md
                  - Freyja Workflow Series: workflows/genomic_characterization/freyja.md
                  - kSNP3: workflows/phylogenetic_construction/ksnp3.md
                  - kSNP4: workflows/phylogenetic_construction/ksnp4.md
                  - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
                  - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md
                  - Nextclade_Batch: workflows/phylogenetic_placement/nextclade_batch.md
                  - Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
                  - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
                  - Terra_2_ENA: workflows/public_data_sharing/terra_2_ena.md
                  - Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md
                  - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
                  - TheiaCoV™ Workflow Series: workflows/genomic_characterization/theiacov.md
                  - TheiaViral™ Workflow Series: workflows/genomic_characterization/theiaviral.md
                  - Usher: workflows/phylogenetic_placement/usher.md
                  - VADR_Update: workflows/genomic_characterization/vadr_update.md
          - Workflows Alphabetically:
              - Overview Table: workflows_overview/workflows_alphabetically.md
              - AMR_Search: workflows/standalone/amr_search.md
              - Assembly_Fetch: workflows/data_import/assembly_fetch.md
              - Augur: workflows/phylogenetic_construction/augur.md
              - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
              - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
              - Clair3_Variants_ONT: workflows/phylogenetic_construction/clair3_variants.md
              - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
              - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
              - Core_Gene_SNP: workflows/phylogenetic_construction/core_gene_snp.md
              - Create_Terra_Table: workflows/data_import/create_terra_table.md
              - Dorado_Basecalling: workflows/standalone/dorado_basecalling.md
              - Fetch_SRR_Accession: workflows/data_import/fetch_srr_accession.md
              - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
              - Freyja Workflow Series: workflows/genomic_characterization/freyja.md
              - GAMBIT_Query: workflows/standalone/gambit_query.md
              - Kraken2: workflows/standalone/kraken2.md
              - kSNP3: workflows/phylogenetic_construction/ksnp3.md
              - kSNP4: workflows/phylogenetic_construction/ksnp4.md
              - Lyve_SET: workflows/phylogenetic_construction/lyve_set.md
              - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
              - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md
              - Metabuli: workflows/standalone/metabuli.md
              - Microreact_Export: workflows/data_export/microreact_export.md
              - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
              - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
              - Nextclade_Batch: workflows/phylogenetic_placement/nextclade_batch.md
              - ONT_Barcode_Concatenation: workflows/data_import/ont_barcode_concatenation.md
              - Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
              - PhyloCompare: workflows/standalone/phylocompare.md
              - RASUSA: workflows/standalone/rasusa.md
              - Rename_FASTQ: workflows/standalone/rename_fastq.md
              - Snippy_Streamline: workflows/phylogenetic_construction/snippy_streamline.md
              - Snippy_Streamline_FASTA: workflows/phylogenetic_construction/snippy_streamline_fasta.md
              - Snippy_Tree: workflows/phylogenetic_construction/snippy_tree.md
              - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
              - SRA_Fetch: workflows/data_import/sra_fetch.md
              - TBProfiler_tNGS: workflows/standalone/tbprofiler_tngs.md
              - Terra_2_ENA: workflows/public_data_sharing/terra_2_ena.md
              - Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md
              - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
              - TheiaCoV™ Workflow Series: workflows/genomic_characterization/theiacov.md
              - TheiaEuk™ Workflow Series: workflows/genomic_characterization/theiaeuk.md
              - TheiaMeta™: workflows/genomic_characterization/theiameta.md
              - TheiaProk™ Workflow Series: workflows/genomic_characterization/theiaprok.md
              - TheiaValidate™: workflows/standalone/theiavalidate.md
              - TheiaViral™ Workflow Series: workflows/genomic_characterization/theiaviral.md
              - Transfer_Column_Content: workflows/data_export/transfer_column_content.md
              - Usher: workflows/phylogenetic_placement/usher.md
              - VADR_Update: workflows/genomic_characterization/vadr_update.md
              - Zip_Column_Content: workflows/data_export/zip_column_content.md
      - Contributing:
          - Contributing to the Documentation: contributing/doc_contribution.md
          - Contributing to the Code: contributing/code_contribution.md

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