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Commit 1bdd3a79 authored by mjbonifa's avatar mjbonifa
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(docs) fixed config.yaml references in readme and docs

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......@@ -189,7 +189,7 @@ cp -r ./examples/concepts/* ./workspace/phen/concepts
From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory:
```bash
cp -r ./examples/config1.yaml ./workspace/phen/config.yaml
cp -r ./examples/config1.yml ./workspace/phen/config.yml
```
- You can view the configuarion file here [`config.json`](./examples/config.json)
......
......@@ -71,13 +71,13 @@ workspace/ # Default workspace directory
│ │ ├── omop/ # Processed phenotype concept sets in OMOP CDM database exported as CSV files
│ ├── map/ # Process mapping from source to target code types
│ │ ├── errors/ # Errors recorded during mapping process
│ ├── config.yaml # Phenotype configuration file
│ ├── vocab_versions.yaml # Versions file for vocabularies used to generate concept sets
│ ├── config.yml # Phenotype configuration file
│ ├── vocab_versions.yml # Versions file for vocabularies used to generate concept sets
```
### **Configuration File**
Each phenotype is defined by configuration is stored in the root of the phenotype directory in `config.yaml`. The file is yaml format.
Each phenotype is defined by configuration is stored in the root of the phenotype directory in `config.yml`. The file is yaml format.
#### **Root Phenotype Element**
- `phenotype`: **(object)** The root element containing all phenotype-related concept sets and metadata.
......
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