mkdocs.yml

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/

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
     - 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
               - 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
               - 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
               - CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.md
               - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
               - kSNP3: workflows/phylogenetic_construction/ksnp3.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:
               - Samples_to_Ref_Tree: workflows/phylogenetic_placement/samples_to_ref_tree.md
               - Usher_PHB: workflows/phylogenetic_placement/usher.md
            - Public Data Sharing:
               - Fetch_SRR_Accession: workflows/public_data_sharing/fetch_srr_accession.md
               - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.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
            - Standalone:
               - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
               - Concatenate_Illumina_Lanes: workflows/standalone/concatenate_illumina_lanes.md
               - GAMBIT_Query: workflows/standalone/gambit_query.md
               - Kraken2: workflows/standalone/kraken2.md
               - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
               - NCBI-Scrub: workflows/standalone/ncbi_scrub.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:
               - Assembly_Fetch: workflows/data_import/assembly_fetch.md
               - BaseSpace_Fetch: workflows/data_import/basespace_fetch.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
               - Kraken2: workflows/standalone/kraken2.md
               - NCBI-Scrub: workflows/standalone/ncbi_scrub.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
               - 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_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
               - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
               - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.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
               - CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.md
               - Freyja Workflow Series: workflows/genomic_characterization/freyja.md
               - kSNP3: workflows/phylogenetic_construction/ksnp3.md
               - MashTree_FASTA: workflows/phylogenetic_construction/mashtree_fasta.md
               - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md
               - Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
               - Samples_to_Ref_Tree: workflows/phylogenetic_placement/samples_to_ref_tree.md
               - Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.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
               - Usher_PHB: workflows/phylogenetic_placement/usher.md
               - VADR_Update: workflows/genomic_characterization/vadr_update.md
        - Workflows Alphabetically: 
            - Overview Table: workflows_overview/workflows_alphabetically.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
            - 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
            - CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.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
            - 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
            - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
            - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
            - Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
            - RASUSA: workflows/standalone/rasusa.md
            - Rename_FASTQ: workflows/standalone/rename_fastq.md
            - Samples_to_Ref_Tree: workflows/phylogenetic_placement/samples_to_ref_tree.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_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
            - Transfer_Column_Content: workflows/data_export/transfer_column_content.md
            - Usher_PHB: 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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