There are 3 ways of specifying which `.ttl` files to include:
* The `tsv_catalog_file` uses the format as created by the [Ontology Catalog Reader](https://gitlab.com/allotrope-open-source/allotrope-devops/-/wikis/The-Ontology-Catalog-Reader). The optional `excludes` parameter can be used to skip files that belong to certain catalog groups.
* The `json_file_list` uses the format `{ "files" : [ "file1.ttl", "file2.ttl" ] }`. The `excludes` parameter will be ignored.
* If no list of files is given, all files from `ontology_path` are used.