ACMC has a five step workflow to create a phenotype including steps initialise, validate, map, publish and export
### Step 1: Initialise
The `initialise` step creates a phenotype directory within the acmc workspace. The outcome will be a directory with all
required subdirectories and files, see [directory structure](#phenotype-directory-structure)
```bash
acmc phen init
```
### Step 2: Validate
The `validate` step checks that the phenotype configuration is valid including verification of the
configuration file according to schema and consistency between concept sets and source concept coding lists. The outcome will be notifications of the validity of the phenotype configuration.
```bash
acmc phen validate
```
### Step 3: Map
The `map` step performs code translations between source and target coding types. The outcome will be a concept sets defined for the target coding types stored in CSV files.
```bash
acmc phen map
```
### Step 4: Publish
The `publish` step commits the phenotype to a git repo and increments the version number. The outcome will be a published phenotype at the next version number
```bash
acmc phen publish
```
### Step 5: Export
The `export` step creates an OMOP database for the phenotype. The outcome will be an OMOP database including concept sets for all target coding types exported as CSV files
