Merge pull request #18 from Sydney-Informatics-Hub/dev-update-session-2

Merge session 2 parts 2.0, 2.1, 2.2 ready for collaborator review

Author: calizilla

docs/assets/2.1_input_help.png

@@ -1,43 +1,39 @@
-# 2.0 Introduction to session 2
+# 2.0 Introduction to Session 2
 
-This session builds on fundamental concepts learned in [Session 1](1.0_intro.md) and provides you with hands-on experience in nf-core workflow customisation. Throughout the session we will be working with data from a [published RNAseq study](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2801-4) and the [nf-core/rnaseq pipeline](https://nf-co.re/rnaseq/3.11.1). 
+This session builds on [Session 1](../session_1/1.0_intro.md), where we explored the core features of nf-core and Nextflow and learnt the fundamental commands and options for executing nf-core pipelines:
 
-We will explore the pipeline source code and apply various customisations using a parameter file and custom configuration files. You will:
+- nf-core is a curated set of analysis pipelines built using the workflow language Nextflow
+- nf-core pipelines are composed of a modular collection of workflows, subworkflows, and modules (processes) where each process performs a discrete analysis task
+- The run can be customised with pipeline parameters (`--`), Nextflow parameters (`-`), and custom configuration files
+- Nextflow `run` command starts the workflow
+- Nextflow `log` can be used to inspect run details
+    
+At the end of session 1, we downloaded the [nf-core/rnaseq](https://nf-co.re/rnaseq/3.23.0) pipeline and submitted our first run. 
+
+During Session 2, we will continue with this pipeline, using the same data from a [published mouse RNAseq study](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2801-4). Pipeline outputs and source code will be explored, and various customisations will be applied using parameters and configuration files to provide you with hands-on experience in nf-core pipeline customisation.
 
-* Create these files for our case study 
-* Use the nf-core tools utility 
-* Run Nextflow commands to query work directories and configuration files 
-* Write some custom Bash code to efficiently extract information from the source code  
 
-Each lesson in this session will build on the previous lessons, so you can gain a deeper understanding of the customisation techniques and the impact they have on the workflow and your results :nerd_face:
 
 !!! note "Applying what you learn here to other nf-core workflows"
 
-    While all activities in this session will be performed using the nf-core/rnaseq workflow, all customisation scenarios we explore are applicable to other nf-core workflows and do not require an understanding of RNAseq data processing. 
+    While all activities in this session use the nf-core/rnaseq workflow, the customisation scenarios we explore are applicable to other nf-core workflows and do not require an understanding of RNA-seq data processing.
+    These skills transfer to other nf-core pipelines thanks to Nextflow as a domain-specific workflow language designed to make workflows portable, and the [nf-core specifications](https://nf-co.re/docs/specifications) placing a strong emphasis on modularity and consistency in code and architecture.
+
 
-## 2.0.1 Log back in to your instance
+<br>
 
-Follow [set up instructions](../setup.html) to log back into your instance in either VS Code or your terminal. 
+!!! example "Exercise 2.0.1 :stopwatch: 2 mins"
 
-In VS Code: 
+    Follow the [set up instructions](../setup.md) to log back into your Nectar VM in either VS Code or your terminal. 
 
-1. Type `Ctrl` + `Shift` + `P` to open command palette and select `Remote-SSH: Connect to Host` and `nfcoreWorkshop`
-2. Type in your provided password (see the Slack channel for the password) and hit enter
+    In VS Code: 
 
-**OR** 
+    1. Type `Ctrl` + `Shift` + `P` to open command palette and select `Remote-SSH: Connect to Host`
+    2. Select the IP address for your VM from the drop-down list
+    3. Type in your provided password and hit enter
 
-In a terminal application:
+    Change into the session 2 directory created in the previous session: 
 
-1. Type the following into your terminal, using your allocated instance’s IP address:
     ```default
-    ssh training@146.118.XXX.XX
+    cd session2
     ```
-2. Type in your provided password (see the Slack channel for the password) and hit enter
-
-## 2.0.2 Create a new work directory
-
-Create a new directory for all session 2 activities and move into it: 
-
-```default
-mkdir ~/session2 && cd $_
-```