Merge pull request #1 from Sydney-Informatics-Hub/fred

AMSI updates

README.md

@@ -2,13 +2,6 @@
 
 Training materials for SIH's implementation of Seqera's Hello Nextflow workshop 2024.
 
-Event description [here](https://www.biocommons.org.au/events/hello-nextflow).
+Event description [here](https://bis.amsi.org.au/speakers/hello-nextflow/).
 
 Content published at: [https://sydney-informatics-hub.github.io/hello-nextflow/](https://sydney-informatics-hub.github.io/hello-nextflow/)
-
-## Run thorugh our self-directed materials
-[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/new/#https://github.com/Sydney-Informatics-Hub/hello-nextflow)
-
-## Developers 
-
-See [set up instructions](./dev_setup/README.md)

docs/content/00_intro.md

@@ -1,15 +1,16 @@
 # Welcome
 
-In **Part 1** of this workshop, you will create a toy multi-step Nextflow workflow.
+In this workshop, you will create a toy multi-step Nextflow workflow.
 
-We will start Part 1 by familiarizing ourselves with some common bash commands. Next, we will turn these commands into a small single-step Nextflow pipeline that will print a greeting to our terminal. In a series of exercises, we will then iterate on this pipeline to make it more flexible using variable outputs, inputs, and parameters. Finally, we will add a second step to the pipeline to dynamically turn our greeting into uppercase letters and name pipeline outputs.
+We will start by familiarizing ourselves with some common bash commands. Next, we will turn these commands into a small single-step Nextflow pipeline that will print a greeting to our terminal. In a series of exercises, we will then iterate on this pipeline to make it more flexible using variable outputs, inputs, and parameters.
 
-During **Part 2**, the skills and concepts you have learned in Part 1 will be applied in a more realistic scenario.
+As a bonus, we will add a second step to the pipeline to dynamically turn our greeting into uppercase letters and name pipeline outputs.
 
 ## Moving into your work directory  
 
 It is good practice to organize projects into their own folders to make it easier to track and replicate experiments over time.
-We have created separate directories for each part (`~/part1/` and `~/part2/`).
+
+For this workshop, all work will be conducted in the `~/part1/` folder.
 
 !!!question "Exercise"
 

docs/index.md

@@ -1,24 +1,27 @@
-# Hello Nextflow workshop 
+# Hello Nextflow!
 
-This workshop will provide you with the foundational knowledge required to build Nextflow workflows. The content is broken up into 2 parts. In the first part we will cover the basic principles for developing Nextflow pipelines. In the second part we will step through building our own Nextflow workflow. See the lesson plan for details.
+This workshop will put you on the path to writing your own reproducible and scalable scientific workflows using Nextflow. You will learn how to use core Nextflow components to build, run and troubleshoot a simple multi-step workflow.  
+
+
+## Trainers  
 
-## Trainers
 * Fred Jaya, Sydney Informatics Hub, University of Sydney
 * Ziad Al Bkhetan, Australian BioCommons
 * Georgie Samaha, Sydney Informatics Hub, University of Sydney
 
-## Prerequisites
+## Prerequisites  
 
-This is an intermediate-advanced workshop for people developing reproducible bioinformatics workflows.
+This is an intermediate workshop for people developing reproducuble bioinformatics workflows.
 
-* Experience working on the command line/Linux environment.
-* Experience developing reproducible workflows (e.g., bash, CWL, WDL, or Snakemake). 
+* Command line and linux skills are essential. The workshop will be conducted in a Unix environment.  
+* (Strongly recommended) Experience developing reproducible workflows (e.g., bash, CWL, WDL, or Snakemake).  
 
-## Set up requirements
+## Set up requirements  
 
 Please complete the [Setup](setup.md) instruction before the workshop. If you have any trouble, please get in contact with us ASAP via Slack.
 
-## Code of Conduct
+## Code of Conduct  
+
 In order to foster a positive and professional learning environment we encourage the following kinds of behaviours at all our events and on our platforms:
 
 * Use welcoming and inclusive language
@@ -30,6 +33,18 @@ In order to foster a positive and professional learning environment we encourage
 
 ## Workshop schedule  
 
+| Time (AEDT) | Activity                           |
+| ----------- | ---------------------------------- |
+| 13:00       | Welcome and set up                 |
+| 13:20       | Introduction to Nextflow           |
+| 13:30       | Bioinformatics demo                |
+| 13:40       | Workshop sections 1-2              |
+| 14:30       | BREAK                              |
+| 15:00       | Workshop sections 3-4              |
+| 15:50       | Where to next?                     |
+| 16:00       | Workshop end                       |
+
+
 ## Credits and acknowledgements
 
 This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera. The workshop was enabled through the Australian BioCommons - [BioCLI Platforms Project](https://www.biocommons.org.au/biocli) (NCRIS via Bioplatforms Australia). 

mkdocs.yml

@@ -7,14 +7,13 @@ nav:
   - Setup: setup.md
   - Workshop content:  
     - 0. Introduction: content/00_intro.md
-    - 1. Why Nextflow?: content/01_hellonextflow.md
-    - 2. Hello World!: content/02_helloworld.md
-    - 3. Your first pipeline: content/03_hellonf.md
-    - 4. Outputs: content/04_output.md
-    - 5. Inputs: content/05_inputs.md
-    - 6. Parameters: content/06_params.md
-    - 7. Adding processes: content/07_process.md
-    - 8. Dynamic naming: content/08_dynamic.md
+    - 1. Hello World!: content/02_helloworld.md
+    - 2. Your first pipeline: content/03_hellonf.md
+    - 3. Outputs: content/04_output.md
+    - 4. Inputs: content/05_inputs.md
+    - 5. Parameters: content/06_params.md
+    - 6. Adding processes: content/07_process.md
+    - 7. Dynamic naming: content/08_dynamic.md
   - Supporting materials: resources.md
 
 theme: