ROOT: data
r_env : scib-R4.0
py_env : scib-pipeline-R4.0

unintegrated_metrics: false

FEATURE_SELECTION:
  #hvg: 2000
  full_feature: 0

SCALING:
  - unscaled
  #- scaled

METHODS:
# python methods
  bbknn:
    output_type: knn
  combat:
    output_type: full
  #desc:
  #  output_type: embed
#  mnn:
#    output_type: full
  #saucie:
  #  output_type:
  #    - full
  #    - embed
  scanorama:
    output_type:
      - embed
      - full
  scanvi:
    output_type: embed
    no_scale: true
    use_celltype: true
  scgen:
    output_type: full
    use_celltype: true
  scvi:
    no_scale: true
    output_type: embed
  #trvae:
  #  no_scale: true
  # output_type:
  #    - embed
  #    - full
  # trvaep:
  #   no_scale: true
  #   output_type:
  #     - embed
  #     - full
# R methods
  #conos: # temporary directory issue
  #  R: true
  #  output_type: knn
  fastmnn:
    R: true
    output_type:
      - embed
      - full
  harmony:
    R: true
    output_type: embed
  liger:
    no_scale: true
    R: true
    output_type: embed
  seurat:
    R: true
    output_type: full
  seuratrpca:
      R: true
      output_type: full

DATA_SCENARIOS:
  test_data_r4:
    batch_key: batch
    label_key: celltype
    organism: mouse
    assay: expression
    file: data/adata_norm.h5ad