merge.yaml

---
configuration:
  output_directory: data/merged
  checkpoint: false

merged_graph:
  name: project_name graph
  source:
    chebi:
      name: "CHEBI"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/chebi_nodes.tsv
          - data/transformed/ontologies/chebi_edges.tsv
    envo:
      name: "ENVO"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/envo_nodes.tsv
          - data/transformed/ontologies/envo_edges.tsv
    chebi_to_reactome:
      name: "CHEBI to Reactome Pathways"
      input:
        format: tsv
        filename:
          - data/transformed/reactome/chebi2reactome_nodes.tsv
          - data/transformed/reactome/chebi2reactome_edges.tsv
  operations:
    - name: kgx.graph_operations.summarize_graph.generate_graph_stats
      args:
        graph_name: project_name graph
        filename: merged_graph_stats.yaml
        node_facet_properties:
          - provided_by
        edge_facet_properties:
          - provided_by
          - source
  destination:
    merged-kg-tsv:
      format: tsv
      compression: tar.gz
      filename: merged-kg
    merged-kg-nt:
      format: nt
      compression: gz
      filename: project_name.nt.gz