From f2bfc24aa11534159d88404396d23a71b6f32a41 Mon Sep 17 00:00:00 2001
From: trhallam <8454087+trhallam@users.noreply.github.com>
Date: Tue, 11 Jun 2024 10:52:35 +0100
Subject: [PATCH] fix navigation level of sections

---
 episodes/10-hpc-intro.Rmd       |  4 ++--
 episodes/11-connecting.Rmd      |  4 +---
 episodes/13-navigation.Rmd      | 12 ++++++++++++
 episodes/15-wildcards-pipes.Rmd |  4 +++-
 4 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/episodes/10-hpc-intro.Rmd b/episodes/10-hpc-intro.Rmd
index cd9720f..3580bb0 100644
--- a/episodes/10-hpc-intro.Rmd
+++ b/episodes/10-hpc-intro.Rmd
@@ -19,10 +19,10 @@ config <- yaml.load_file("lesson_config.yaml")
   - Identify how an HPC system could benefit you.
 ::::::
 
-# Why Use These Computers?
+## Why Use These Computers?
 
 ::: challenge
-## What do you need?
+### What do you need?
 
 Talk to your neighbour about your research. How does computing help you do
 your research? How could more computing help you do more or better research?
diff --git a/episodes/11-connecting.Rmd b/episodes/11-connecting.Rmd
index 5d18360..0c54575 100644
--- a/episodes/11-connecting.Rmd
+++ b/episodes/11-connecting.Rmd
@@ -20,7 +20,7 @@ snippets <- paste('files/snippets/', config$snippets, sep='')
   - Connect to a remote HPC system.
 ::::::
 
-# Opening a Terminal
+## Opening a Terminal
 
 Connecting to an HPC system is most often done through a tool known as "SSH"
 (Secure SHell) and usually SSH is run through a terminal. So, to begin using an
@@ -276,5 +276,3 @@ ssh yourUsername@remote.computer.address
 ssh -i ~/.ssh/key_for_remote_computer yourUsername@remote.computer.address
 ```
 ::::::
-
-
diff --git a/episodes/13-navigation.Rmd b/episodes/13-navigation.Rmd
index 24b1cf1..dab2318 100644
--- a/episodes/13-navigation.Rmd
+++ b/episodes/13-navigation.Rmd
@@ -21,6 +21,8 @@ config <- yaml.load_file("lesson_config.yaml")
   - Demonstrate the use of tab completion, and explain its advantages.
 ::::::
 
+## First commands
+
 At this point in the lesson, we've just logged into the system. Nothing has
 happened yet, and we're not going to be able to do anything until we learn a
 few basic commands. By the end of this lesson, you will know how to "move
@@ -72,6 +74,8 @@ $ pwd
 `r config$remote$homedir`yourUsername
 ```
 
+## List directory contents
+
 So, we know where we are. How do we look and see what's in our current
 directory?
 ```bash
@@ -102,6 +106,8 @@ you are issuing commands on when in the shell.
 
 :::
 
+## Making directories
+
 If nothing shows up when you run `ls`, it means that nothing's there. Let's
 make a directory for us to play with.
 
@@ -128,6 +134,8 @@ $ pwd
 ~/documents
 ```
 
+## The tilde ~
+
 What is the `~` character? When using the shell, `~` is a shortcut that
 represents ``r config$remote$homedir`yourUserName`.
 
@@ -196,6 +204,8 @@ File storage locations:
  against your job's memory usage and be deleted at the end of your job.
 :::
 
+## Navigation shortcuts
+
 There are several other useful shortcuts you should be aware of.
 
 - `.` represents your current directory
@@ -216,6 +226,8 @@ $ pwd
 `r config$remote$homedir`yourUserName
 ```
 
+## Command flags and options
+
 Many commands also have multiple behaviours that you can invoke with command
 line 'flags.' What is a flag? It's generally just your command followed by a
 '-' and the name of the flag (sometimes it's '--' followed by the name of the
diff --git a/episodes/15-wildcards-pipes.Rmd b/episodes/15-wildcards-pipes.Rmd
index add4cdc..c3e75c1 100644
--- a/episodes/15-wildcards-pipes.Rmd
+++ b/episodes/15-wildcards-pipes.Rmd
@@ -67,8 +67,10 @@ SRR307025_1.fastq                            SRR307030_1.fastq
 SRR307025_2.fastq                            SRR307030_2.fastq
 ```
 
+## Word counts and wildcards (globbing)
+
 Now we have a whole bunch of example files in our directory. For this example
-we are going to learn a new command that tells us how long a file is: `wc`. `wc-l file` 
+we are going to learn a new command that tells us how long a file is: `wc`. `wc -l file` 
 tells us the length of a file in lines.
 
 ```bash