%%metro title: nf-core/reportho
%%metro style: dark
%%metro line: main | Main flow | #24b064
%%metro line: report | Report flow | #0dcaf0
%%metro line: samplesheets | Samplesheet flow | #f59e0b
%%metro legend: bl

%%metro file: id_in | ID | Uniprot ID
%%metro file: fasta_in | FASTA | Protein sequence
%%metro file: query_reports | HTML | Per-query reports
%%metro file: msa_samplesheet | CSV | MSA samplesheet

graph LR
    subgraph input [Input]
        id_tax [Identify taxon]
    end

    subgraph fetch_seqs [Fetch sequences]
        source_merge [Merge sequences]
    end

    subgraph score_orthologs [Score orthologs]
        make_score_table [Make score table]
        make_plots [Make plots]
        filter_hits [Filter hits]

        make_score_table -->|main| filter_hits
        make_score_table -->|main| make_plots
    end

    subgraph create_samplesheets [Create samplesheets]
        create_msa [Create MSA samplesheet]
        msa_samplesheet [ ]

        create_msa -->|samplesheets| msa_samplesheet
    end

    subgraph report [Report]
        generate_reports [Generate reports]
        query_reports [ ]

        generate_reports -->|main| query_reports
    end

    %% inter-section connectors
    id_tax -->|main| source_merge
    source_merge -->|main| make_score_table
    make_plots -->|main| generate_reports

    %% either of the connections below works, but not both at once
    source_merge -->|samplesheets| create_msa
    %% filter_hits -->|samplesheets| create_msa