config.yml

# target directory
output_dir: /project/kleinman/hussein.lakkis/from_hydra/test
# path to reference to train classifiers on (cell x gene raw counts)
training_reference: /project/kleinman/hussein.lakkis/from_hydra/2022_01_10-Datasets/Cortex/p0/expression.csv
# path to annotations for the reference (csv file with cellname and label headers)
reference_annotations: /project/kleinman/hussein.lakkis/from_hydra/2022_01_10-Datasets/Cortex/p0/labels.csv
# path to query datasets (cell x gene raw counts)
query_datasets:
      - /project/kleinman/hussein.lakkis/from_hydra/Collab/HGG_Selin_Revision/test/BT2016062/expression.csv
      - /project/kleinman/hussein.lakkis/from_hydra/Collab/HGG_Selin_Revision/test/P-1694_S-1694_multiome/expression.csv
      - /project/kleinman/hussein.lakkis/from_hydra/Collab/HGG_Selin_Revision/test/P-1701_S-1701_multiome/expression.csv
# step to check if some genes are kept in the common gene space between ref and query
check_genes: False
# path for the genes required
genes_required: Null
# rejection option for SVM
rejection: True
# classifiers to run
tools_to_run:
      - ACTINN
      - scHPL
      - scClassify
      - correlation
      - scmapcluster
      - scPred
      - SingleCellNet
      - SVM_reject
      - SingleR
      - CHETAH
      - scmapcell
      - SciBet
# benchmark tools on reference
benchmark: False
plots: True
consensus:
      - all