preamble:
   input_reference_genome: hs1/genomes/ucsc-hs1
   summary: Clinical Annotation Pipeline for hs1
   description: This pipeline annotates T2T-CHM13/hs1 variants with clinical resources.
   
annotators:

- liftover_annotator:
    chain: liftover/hs1_to_hg38
    attributes:
    - name: hg38_annotatable 
      source: liftover_annotatable
      internal: true

- effect_annotator:
    gene_models: hg38/gene_models/MANE/1.5 
    input_annotatable: hg38_annotatable
    attributes:
    - name: worst_effect_MANE_1.5
      source: worst_effect 
    - name: effect_details_MANE_1.5
      source: effect_details 
    - name: gene_effects_MANE_1.5
      source: gene_effects 


- normalize_allele_annotator:
    genome: hg38/genomes/GRCh38-hg38
    input_annotatable: hg38_annotatable

- allele_score_annotator:
    resource_id: hg38/scores/dbSNP
    input_annotatable: normalized_allele
    attributes:
    - name: dbSNP_rs_number
      source: RS 

- allele_score_annotator:
    resource_id: hg38/variant_frequencies/gnomAD_4.1.0/exomes/ALL
    input_annotatable: normalized_allele

- allele_score_annotator:
    resource_id: hg38/variant_frequencies/gnomAD_4.1.0/genomes/ALL
    input_annotatable: normalized_allele

- allele_score_annotator:
    resource_id: hg38/scores/ClinVar_20251019
    input_annotatable: normalized_allele
    attributes:
    - name: clinical_significance
      source: CLNSIG    
    - name: clinical_disease_name
      source: CLNDN 

- position_score_annotator:
    resource_id: hg38/scores/phyloP7way
    input_annotatable: normalized_allele
    attributes:
    - name: phyloP7way
      source: phyloP7way

- allele_score_annotator:
    resource_id: hg38/scores/AlphaMissense
    input_annotatable: normalized_allele
    attributes:
    - name: AlphaMissense_pathogenicity
      source: am_pathogenicity
    - name: AlphaMissense_class
      source: am_class 

- liftover_annotator:
    chain: liftover/hs1_to_hg19
    attributes:
    - source: liftover_annotatable
      name: hg19_annotatable
      internal: true

- allele_score_annotator:
    resource_id: hg19/scores/MPC
    input_annotatable: hg19_annotatable

- effect_annotator:
    gene_models: hg38/gene_models/GENCODE/49/basic/ALL
    genome: hg38/genomes/GRCh38-hg38
    input_annotatable: hg38_annotatable
    attributes:
    - name: worst_effect_GENCODE_49
      source: worst_effect 
    - name: effect_details_GENCODE_49
      source: effect_details 
    - name: gene_effects_GENCODE_49
      source: gene_effects 
    - name: gene_list 
      internal: true


- gene_score_annotator:
    resource_id: gene_properties/gene_scores/pLI
    input_gene_list: gene_list
    attributes:
    - name: pLI_rank_all
      source: pLI_rank
    - name: pLI_rank_min
      source: pLI_rank
      aggregator: min 
      
- gene_score_annotator:
    resource_id: gene_properties/gene_scores/LOEUF
    input_gene_list: gene_list
    attributes:
    - name: LOEUF_rank_all
      source: LOEUF_rank
    - name: LOEUF_rank_min
      source: LOEUF_rank
      aggregator: min 

- effect_annotator:
    gene_models: hs1/gene_models/ncbiRefSeq_20250529
    attributes:
    - worst_effect
    - gene_effects
    - effect_details
