Sanitize redacted name

.vscode/settings.json

@@ -12,6 +12,5 @@
         "limsdatapull",
         "miseq",
         "mkdir",
-        "wphl"
     ]
 }

README.md

@@ -1,10 +1,11 @@
-# wphl-bioinformatics
+# SC2 Sequencing Cheats
 
-Bioinformatics scripts for use at the Wyoming Public Health Laboratory.
+File manipulation/bioinformatics-type scripts that my colleuges have found
+useful in sequencing SARS-CoV2 (SC2).
 
 These scripts have various purposes, uses, and instructions. The only unifying
-thing about them is that they were all written for WPHL. Please check the
+thing about them is that they were all written for SC2 and related sequencing.
-`README` file in each directory for more detailed instructions.
+Please check the `README` file in each directory for more detailed instructions.
 
 ## Encryption
 
@@ -49,7 +50,7 @@ Encryption is GPG-based. If your GPG key has been added to the repository (you
 know if you have access), then run
 
 ```bash
-git clone https://github.com/MillironX/wphl-bioinformatics.git && cd wphl-bioinformatics
+git clone https://github.com/MillironX/sc2-sequencing.git && cd sc2-sequencing
 git-crypt unlock
 ```
 
@@ -57,4 +58,4 @@ The files will now be decrypted and can be usable.
 
 If you need to copy your GPG keys to a new machine to be able to decrypt the
 files, follow the instructions at
-https://www.phildev.net/pgp/gpg_moving_keys.html under "Copy Just Your Keys."
+<https://www.phildev.net/pgp/gpg_moving_keys.html> under "Copy Just Your Keys."

clearlabs/README.md

@@ -22,8 +22,8 @@ This script requires [Cygwin](https://cygwin.com/install.html).
 2. Open the Cygwin console and use the following commands
 
     ```bash
-    git clone https://github.com/MillironX/wphl-bioinformatics.git
+    git clone https://github.com/MillironX/sc2-sequencing.git
-    cp wphl-bioinformatics/clearlabs/convert-fastas.sh ~
+    cp sc2-sequencing/clearlabs/convert-fastas.sh ~
     chmod +x convert-fastas.sh
     ```
 

illumina/README.md

@@ -49,8 +49,8 @@ Cygwin.
 7. In Cygwin console now run
 
     ```bash
-    git clone https://github.com/MillironX/wphl-bioinformatics.git
+    git clone https://github.com/MillironX/sc2-sequencing.git
-    cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
+    cp sc2-sequencing/illumina/dl-fastqs.sh ~
     chmod +x dl-fastqs.sh
     ```
 

limsdatapull/README.md

@@ -4,7 +4,7 @@ Pulls positive SC2 sample IDs and relevant dates from StarLIMS.
 
 **NOTE:** These scripts are encrypted, but are generally intended for use on
 Windows machines. Decrypt them on a Linux/Mac machine using the [entire repo
-instructions](https://github.com/MillironX/wphl-bioinformatics/blob/master/README.md),
+instructions](https://github.com/MillironX/sc2-sequencing/blob/master/README.md),
 then copy over using a secure flash drive or similar method.
 
 ## Usage

ont/README.md

@@ -1,10 +1,11 @@
 # Oxford Nanopore Technologies
 
-These scripts are for use with a GridION, to make the files and folder
+These scripts are for use with a GridION or its output file, to make the files
-structures correspond more closely to those required by downstream
+and folder structures correspond more closely to those required by downstream
 bioinformatics programs. Note that at the time of writing, the GridION runs
 Ubuntu 16.04 LTS, and mounts USB drives in the `/data` folder, and these scripts
-contain some "faults" to work around these idiosyncrasies.
+contain some "faults" to work around these idiosyncrasies (i.e. they will not
+pass in [ShellCheck]).
 
 ## Usage
 
@@ -31,7 +32,7 @@ julia --project=PATH_TO_ONT_FOLDER PATH_TO_ONT-RENAME.jl
 In practice, this looks like
 
 ```powershell
-julia --project=C:\Users\MillironX\ont C:\Users\MillironX\illumina\ont-rename.jl
+julia --project=C:\Users\MillironX\ont C:\Users\MillironX\ont\ont-rename.jl
 ```
 
 ### `ont-demux` (deprecated)
@@ -45,9 +46,9 @@ same results using far fewer resources and in far less time.**
 
 Consolidates all FAST5s into a single gzipped FASTQ using ONT's
 `guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000
-reads/file. It is _highly_ recommended to set the "Number of Reads per File"
+reads/file. ~~It is _highly_ recommended to set the "Number of Reads per File"
 entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same
-results.
+results~~ (this functionality has been taken out of recent updates to MinKNOW).
 
 ## Installation
 
@@ -56,7 +57,7 @@ results.
 #### Requirements
 
 - git
-- guppy (Get from [ONT Community](https://nanoporetech.com/community)
+- guppy (Get from [ONT Community])
 - GNU Parallel
 
 See ONT for guppy installation instructions. Others may be installed by opening
@@ -71,17 +72,19 @@ sudo apt-get install git parallel -y
 Open a terminal (Ctrl+Alt+T), and use the following commands
 
 ```bash
-git clone https://github.com/MillironX/wphl-bioinformatics
+git clone https://github.com/MillironX/sc2-sequencing
 mkdir ~/bin
 echo "export PATH=$PATH:$HOME/bin" >> ~/.bashrc
-cp wphl-bioinformatics/ont/* ~/bin
+cp sc2-sequending/ont/* ~/bin
 chmod +x ~/bin/*
 source ~/.bashrc
 ```
 
 ### `ont-rename`
 
-These scripts require [Julia](https://julialang.org).
+These scripts require [Julia].
+
+Windows install instructions (I will assume Linux users can adapt):
 
 1. Download and install Julia
     1. Select "Add Julia to PATH" as an option
@@ -97,6 +100,10 @@ These scripts require [Julia](https://julialang.org).
 10. Run `exit()`
 11. Close PowerShell
 12. Right-click the Windows desktop, and click "New | Shortcut..."
-13. Type `julia --project=%USERPROFILE%\ont
+13. Type `julia --project=%USERPROFILE%\ont %USERPROFILE%\ont\ont-rename.jl` and
-    %USERPROFILE%\ont\ont-rename.jl` and click Next
+    click Next
 14. Type `Rename ONT FASTQs` or something else memorable and click "Finish"
+
+[ShellCheck]: https://shellcheck.net
+[ONT Community]: https://nanoporetech.com/community
+[Julia]: https://julialang.org