From befca3557e4b5def4084151d71c52e2b6e96799b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 13 Apr 2021 12:50:14 -0600
Subject: [PATCH] Correct and cleanup Illumina README

---
 .vscode/settings.json |  7 ++++++
 illumina/README.md    | 52 +++++++++++++++++++++++++------------------
 2 files changed, 37 insertions(+), 22 deletions(-)
 create mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..840f89a
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,7 @@
+{
+    "cSpell.words": [
+        "chmod",
+        "cygpath",
+        "wphl"
+    ]
+}
\ No newline at end of file
diff --git a/illumina/README.md b/illumina/README.md
index e42b9d1..3888cac 100644
--- a/illumina/README.md
+++ b/illumina/README.md
@@ -1,53 +1,61 @@
 # Illumina
 
-This script downloads all FASTQs associated with a specific Run ID from Illumina's Basespace.
+This script downloads all FASTQs associated with a specific Run ID from
+Illumina's Basespace.
 
 ## Usage
 
 To be run in Cygwin
 
 ```bash
-$ dl-fastqs.sh
+dl-fastqs.sh
 ```
 
-The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina Basespace.
+The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina
+Basespace.
 
-![Illumina Basespace](https://user-images.githubusercontent.com/25492070/113320967-59a88000-92d0-11eb-967c-6b338e247ca5.png)
+![Illumina
+Basespace](https://user-images.githubusercontent.com/25492070/113320967-59a88000-92d0-11eb-967c-6b338e247ca5.png)
 
-Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use right-click, instead.
+Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use
+right-click, instead.
 
 ## Installation
 
-This script requires [Cygwin](https://cygwin.com/install.html). The install process is complicated thanks to requiring native features of both Windows and Cygwin.
+This script requires [Cygwin](https://cygwin.com/install.html). The install
+process is complicated thanks to requiring native features of both Windows and
+Cygwin.
 
 1. Download and install Cygwin
     1. Select "Just Me" when asked who to install for
-    2. Find and add the latest version of the "git" and "xargs" packages
+    2. Find and add the latest version of the "git" packages
     3. All other default options will work
 2. Press `Win+X`, then `I` to open a new PowerShell window
-3. Run `wget  "https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest" -O $env:LOCALAPPDATA\Microsoft\WindowsApps\bs.exe`
+3. Run `wget
+   'https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest'
+   -O $env:LOCALAPPDATA\Microsoft\WindowsApps\bs.exe`
 4. Close PowerShell
 5. Open Cygwin Console and run
 
-```bash
-$ BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
-$ $BS auth
-```
-6. Copy the given link, navigate to it in a browser, and login to Illumina Basespace
+    ```bash
+    BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
+    $BS auth
+    ```
+
+6. Copy the given link, navigate to it in a browser, and login to Illumina
+   Basespace
 7. In Cygwin console now run
 
-```bash
-$ git clone https://github.com/MillironX/wphl-bioinformatics.git
-$ cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
-$ chmod +x dl-fastqs.sh
-```
+    ```bash
+    git clone https://github.com/MillironX/wphl-bioinformatics.git
+    cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
+    chmod +x dl-fastqs.sh
+    ```
 
 8. Right-click the Windows desktop, and click "New | Shortcut..."
 9. Type `C:\cygwin64\bin\bash.exe` and click Next
 10. Type `Download Illumina Run` or something else memorable and click "Finish"
 11. Right-click the newly created shortcut and click Properties
-12. In the Target textbox, add ` --login dl-fastqs.sh` (including the space) to the existing text
+12. In the Target textbox, add a space and `--login dl-fastqs.sh` to the
+    existing text
 13. Click OK
-
-
-