pra.yaml

# Base Settings
# TODO: (same for dmmm.yaml): can we deduplicate this using snakemake?
hash_length: 7
container_framework: docker
unpack_singularity: false

container_registry:
  base_url: docker.io
  owner: reedcompbio

reconstruction_settings:
  locations:
    reconstruction_dir: "output"
    run: true

analysis:
  summary:
    include: false
  graphspace:
    include: false
  cytoscape:
    include: false
  ml:
    include: true
    aggregate_per_algorithm: true
  evaluation:
    include: false

# Custom settings
algorithms:
  - name: "omicsintegrator1"
    params:
      include: true
      run1:
        b: [2]
        w: [.5]
        d: [10]
        mu: [2]
  - name: "omicsintegrator2"
    params:
      include: true
      run1:
        b: [4]
        g: [0]
  - name: "pathlinker"
    params:
      include: true
      run1:
        k: [10, 20]
  - name: "allpairs"
    params:
      include: true

datasets:
  - label: pramuscleskeletal2018
    node_files: ["sources.txt", "targets.txt"]
    # DataLoader.py can currently only load a single edge file, which is the primary network
    edge_files: ["interactome.tsv"]
    # Placeholder
    other_files: []
    # Relative path from the spras directory
    data_dir: "datasets/rn-muscle-skeletal/processed"