config.yaml 798 Bytes
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pathofact:
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  sample: ["test_sample"] # requires user input
  project: PathoFact_update_trial # requires user input
  datadir: ../test_dataset # requires user input
  workflow: "Vir" 
  size_fasta: 1000
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  scripts: "scripts"
  signalp: "/path/to/signalp-4.1/signalp" # requires user input
  deeparg: "submodules/deeparg-ss/deepARG.py"
  deepvirfinder: "submodules/DeepVirFinder/dvf.py"
  tox_hmm: "databases/toxins/combined_Toxin.hmm"
  tox_lib: "databases/library_HMM_Toxins.csv"
  vir_hmm: "databases/virulence/Virulence_factor.hmm"
  vir_domains: "databases/models_and_domains"
  plasflow_threshold: 0.7
  plasflow_minlen: 1000
  runtime:
    short: "00:10:00"
    medium: "01:00:00"
    long: "02:00:00"
  mem:
    normal_mem_per_core_gb: "4G"
    big_mem_cores: 4
    big_mem_per_core_gb: "30G"