When Nextclade CLI calls clades but Nextclade Web does not

1

Posting here in case others run into the same problem.

I was building a Nextclade dataset. During testing the Nextclade CLI called clades while the Nextclade Web left the clades column blank. After chatting with Cornelius realized Nextclade Web had the tree button greyed out, which meant the “tree.json” was not being loaded. In pathogen.json, I was missing a line

  "files": {
    "reference": "reference.fasta",
    "pathogenJson": "pathogen.json",
    "genomeAnnotation": "genome_annotation.gff3",
    "examples": "sequences.fasta",
    "readme": "README.md",
    "changelog": "CHANGELOG.md",
    "treeJson": "tree.json"  #<==== Missing this line, required for Nextclade Web
  },

The Nextclade CLI worked since it was being passed the whole directory (containing the tree.json)

nextclade run \
  example_sequences.fasta \
  --input-dataset minimal-dataset \
  --output-all test_output