Minor formatting updates

README.md

@@ -1,7 +1,7 @@
-# IchorCurate
-IchorCurate is a solution curation application to supplement [ichorCNA](https://github.com/broadinstitute/ichorCNA), a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing (ULP-WGS, 0.1x coverage).
+# ichorCurate
+ichorCurate is a solution curation application to supplement [ichorCNA](https://github.com/broadinstitute/ichorCNA), a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing (ULP-WGS, 0.1x coverage).
 
-As a Streamlit powered app, IchorCurate allows users to seamlessly monitor, collaborate, and execute ichorCNA optimal solution selection.
+As a Streamlit powered app, ichorCurate allows users to seamlessly monitor, collaborate, and execute ichorCNA optimal solution selection.
 
 ## Usage
 After running ichorCNA and generating the potential solution outputs, use the following steps to run this application locally. In future versions, we plan to deploy this app on a server, but currently this app must be run through cloning the repository.
@@ -10,14 +10,14 @@ After running ichorCNA and generating the potential solution outputs, use the fo
 To start, clone this repository. 
 
 ```
-git clone https://github.com/ajnetzley/IchorCurate.git
+git clone https://github.com/ajnetzley/ichorCurate.git
 ```
 
 Next, create a venv with Python 3.11.5, and use the "requirements.txt" to create a virtual environment to run the application in.
 
 ```
-python3.11 -m venv IchorCurate_env
-source IchorCurate_env/bin/activate
+python3.11 -m venv ichorCurate_env
+source ichorCurate_env/bin/activate
 pip install -r requirements.txt
 ```
 
@@ -53,4 +53,4 @@ Next, you are directed to the Tracker Dashboard page, which contains a summary d
 ```
 
 ## Acknowledgments
-IchorCurate is developed by Alexander Netzley, on behalf of the Gavin Ha Lab at Fred Hutch Cancer Center
+ichorCurate is developed by Alexander Netzley, on behalf of the Gavin Ha Lab at Fred Hutch Cancer Center

app.py

@@ -1,10 +1,10 @@
 """
 app.py
-v1.0.0, 11/6/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides the wrapper function for running the IchorCurate app.
+This module provides the wrapper function for running the ichorCurate app.
 """
 
 # Import packages
@@ -21,7 +21,7 @@
 st.set_page_config(layout="wide")
 
 # Title of the app
-st.title('IchorCurate')
+st.title('ichorCurate')
 
 # Initialize session for login
 if "logged_in" not in st.session_state:

pages/curation.py

@@ -1,10 +1,10 @@
 """
 curation.py
-v0.1.0, 11/6/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides the main logic for the curation page of the IchorCurate app.
+This module provides the main logic for the curation page of the ichorCurate app.
 """
 
 # Import packages

pages/folder_selection.py

@@ -1,10 +1,10 @@
 """
 login.py
-v0.1.0, 12/2/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides the logic for the folder selection page of the IchorCurate app.
+This module provides the logic for the folder selection page of the ichorCurate app.
 """
 
 # Import packages
@@ -15,7 +15,7 @@ def display():
     st.title("Folder Selection")
 
     # Input field for folder path
-    folder_path = st.text_input("Enter the path to the IchorCNA data you wish to curate. This should be a path to a folder containing subdirectories named for each sample")
+    folder_path = st.text_input("Enter the path to the ichorCNA data you wish to curate. This should be a path to a folder containing subdirectories named for each sample")
 
     if folder_path:
         # Validate if the folder exists

pages/login.py

@@ -1,10 +1,10 @@
 """
 login.py
-v0.1.0, 11/6/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides the logic for the entry login page of the IchorCurate app.
+This module provides the logic for the entry login page of the ichorCurate app.
 """
 
 # Import packages

pages/tracker_dashboard.py

@@ -1,10 +1,10 @@
 """
 tracker_dashboard.py
-v0.1.0, 11/6/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides the main logic for the tracker dashboard page of the IchorCurate app.
+This module provides the main logic for the tracker dashboard page of the ichorCurate app.
 """
 
 # Import packages

src/utils.py

@@ -1,10 +1,10 @@
 """
 utils.py
-v1.0.0, 11/6/2024
+v0.1.0, 12/9/2024
 Author: Alexander Netzley, [email protected]
 Ha Lab, Fred Hutchinson Cancer Research Center
 
-This module provides helper functions for the IchorCurate app.
+This module provides helper functions for the ichorCurate app.
 """
 # Import packages
 import fitz  # PyMuPDF