From dc326521e5449dfd0d06e766f6fe61cd999f49b9 Mon Sep 17 00:00:00 2001
From: Michael Boniface <mjbonifa@soton.ac.uk>
Date: Fri, 7 Mar 2025 18:13:41 +0000
Subject: [PATCH] (docs) started to write the docstrings

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 1 file changed, 50 insertions(+)

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 # User Guide
 
+- [Phenotype Workflow](#phenotype-workflow)
+- [Phenotype Definition](#phenotype-definition)
+- [Version Control](#version-control)
+
+## Phenotype Workflow
+
+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
+
+```bash
+acmc phen export
+```
+
 ## Phenotype Definition
 
 ### **Phenotype directory structure**
-- 
GitLab