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sacdallago / bio_embeddings

Get protein embeddings from protein sequences
http://docs.bioembeddings.com
MIT License
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Forward references break give a confusing error #121

Open konstin opened 3 years ago

konstin commented 3 years ago 
global:
  prefix: projected_tucker
  sequences_file: bonsai/knn_reference.fasta
bert_embed:
  type: embed
  protocol: prottrans_bert_bfd
  reduce: true
  discard_per_amino_acid_embeddings: true
visualize_bert:
  type: visualize
  protocol: plotly
  depends_on: umap_tucker
  n_components: 2
umap_tucker:
  type: project
  protocol: umap
  depends_on: bert_embed

This (correctly) fails, but instead of triggering the "Stage {} depends on {}, but dependency not found in config." error, it complains about a missing parameter