preamble:
  summary: Demo pipeline 
  description: Demonstrates a GAIn pipeline
  input_reference_genome: hg38/genomes/GRCh38-hg38


annotators:
- effect_annotator:
    gene_models: hg38/gene_models/MANE/1.3
    attributes:
    - worst_effect
    - gene_list
    - genes

- position_score:
    resource_id: hg38/scores/phyloP7way

- normalize_allele_annotator

- allele_score:
    resource_id: hg38/variant_frequencies/gnomAD_4.1.0/exomes/ALL 
    input_annotatable: normalized_allele
    attributes:
    - name: gnomAD_4.1_af
      source: AF

- allele_score: 
    resource_id: hg38/scores/dbNSFP4.9a 
    input_annotatable: normalized_allele
    attributes:
    - MVP_rankscore

- allele_score: 
    resource_id: hg38/scores/ClinVar_20240730 
    input_annotatable: normalized_allele
    attributes:
    - CLNSIG
    - CLNDN

- gene_score_annotator:
    resource_id: gene_properties/gene_scores/pLI
    input_gene_list: gene_list
    attributes:
    - pLI_rank

- gene_set_annotator:
    resource_id: gene_properties/gene_sets/GO_2024-06-17_release
    input_gene_list: gene_list 
    attributes:
    - name: replication fork processing
      source: "GO:0031297" 

- liftover_annotator:
    chain: liftover/hg38ToHg19
    attributes:
    - name: hg19_annotatable 
      source: liftover_annotatable
      internal: true

- position_score:
    resource_id: hg19/scores/fitCons2/E063
    input_annotatable: hg19_annotatable 
