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Commit ce34c5c4 authored by Laura Denies's avatar Laura Denies
Browse files

Update config.yaml

parent 2765df7b
......@@ -2,13 +2,14 @@ pathofact:
sample: ["sample"] # requires user input
project: PathoFact_results # requires user input
datadir: /path/to/dataset # requires user input
workflow: "complete"
size_fasta: 10000
workflow: "complete" #options: "complete", "AMR", "Tox", "Vir"
size_fasta: 10000 #Adjustable to preference
scripts: "scripts"
signalp: "/path/to/signalp-5.0b/bin" # requires user input
deepvirfinder: "submodules/DeepVirFinder/dvf.py"
tox_hmm: "databases/toxins/combined_Toxin.hmm"
tox_lib: "databases/library_HMM_Toxins.csv"
tox_threshold: 40 #Bitscore threshold of the toxin prediction, adjustable by user to preference
vir_hmm: "databases/virulence/Virulence_factor.hmm"
vir_domains: "databases/models_and_domains"
plasflow_threshold: 0.7
......
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