Add sorting scripts to Illumina README

.vscode/settings.json

@@ -4,6 +4,7 @@
         "chmod",
         "cygpath",
         "demux",
+        "miseq",
         "mkdir",
         "wphl"
     ]

illumina/README.md

@@ -1,9 +1,11 @@
 # Illumina
 
+## FASTQ Downloader
+
 This script downloads all FASTQs associated with a specific Run ID from
 Illumina's Basespace.
 
-## Usage
+### Usage
 
 To be run in Cygwin
 
@@ -20,7 +22,7 @@ Basespace](https://user-images.githubusercontent.com/25492070/113320967-59a88000
 Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use
 right-click, instead.
 
-## Installation
+### Installation
 
 This script requires [Cygwin](https://cygwin.com/install.html). The install
 process is complicated thanks to requiring native features of both Windows and
@@ -59,3 +61,48 @@ Cygwin.
 12. In the Target textbox, add a space and `--login dl-fastqs.sh` to the
     existing text
 13. Click OK
+
+## FASTQ Sorters
+
+These scripts change the file names of the FASTQ files to correspond with the
+well positions during prep phases.
+
+### Usage
+
+To be run with Julia.
+
+```powershell
+julia --project=PATH_TO_ILLUMINA_FOLDER PATH_TO_SORTING_SCRIPT
+```
+
+In practice, this looks like
+
+```powershell
+julia --project=C:\Users\MillironX\illumina C:\Users\MillironX\illumina\sort-miseq.jl
+```
+
+### Installation
+
+These scripts require [Julia](https://julialang.org).
+
+1. Download and install Julia
+    1. Select "Add Julia to PATH" as an option
+    2. All other default options will work
+2. Download the Repo's ZIP file (click green button on upper-right)
+3. Press `Win+R`, type `%USERPROFILE%` and press Enter
+4. Copy the illumina folder from the ZIP file into the newly opened folder
+5. Press `Win+X`, then `I` to open a new PowerShell window
+6. Type `julia --project=$env:USERPROFILE\illumina` and press Enter
+7. Press the `]` key, the prompt should change to say `(illumina) pkg>`
+8. Run `instantiate`
+9. Press the backspace key to return to the `julia>` prompt
+10. Run `exit()`
+11. Close PowerShell
+12. Right-click the Windows desktop, and click "New | Shortcut..."
+13. Type `julia --project=%USERPROFILE%\illumina
+    %USERPROFILE%\illumina\sort-miseq.jl` and click Next
+14. Type `Sort MiSeq Run` or something else memorable and click "Finish"
+15. Right-click the Windows desktop, and click "New | Shortcut..."
+16. Type `julia --project=%USERPROFILE%\illumina
+    %USERPROFILE%\illumina\sort-nextseq.jl` and click Next
+17. Type `Sort NextSeq Run` or something else memorable and click "Finish"