Learning Journey

December 4^th

Local infrastructure and resources:
- Guide to online and accessble virtual environments and coding spaces
- Exploration and installation of Gitpod/Codespace
- Verification and configuration of personal Telethon Kids Institute VMs
- Provide Biowiki resources and relevant guides and information

December 5^th

Introduction to nf-core:
- What is nf-core?
- How does nf-core work?
- What are community best practices?
- Where can you go to find this information?
- Where can you go to get one-on-one help?
- Overview of available tools
Toy pipeline development:
To show the basic structures of pipelines (not nf-core style)
- Making a small pipeline
  - Make first process and a workflow block
  - Make a second process and join with the operators
    - Include metadata
  - Add a container for software
  - Use directives to allocate resources
nf-core repository, configurations, and deploying pipelines
- Structures of nf-core repositories
- Building run commands using demo pipelines
- Where are configs found and what are their orders of priority:
  - Deploying pipeline with custom parameters
  - Deploying pipeline with custom params files
  - Deploying pipeline wth config file and selectors
  - What could be conflicting results?

December 6^th

nf-core repository, configurations, and deploying pipelines Continuation
nf-core/fetchngs and nf-core/rnaseq:
- Focusing on usage of these specific pipelines
- Running the pipelines with various parameter choices
- Configurations and pipeline parameters specific to your data
- Recognition of resources and troubleshooting
December 7^th
nf-core/mag and nf-core/ampliseq:
- Focusing on usage of these specific pipelines, with a microbiome focus
- Running the pipelines with various parameter choices
- Configurations and pipeline parameters specific to your data
- Recognition of resources and troubleshooting
Building nf-core pipeline and customisation
- Creating an nf-core pipeline with custom input data
- Adding modules and subworkflows to the custom pipeline
- Adding logics to include and exclude subworkflows being executed
- Adding local modules and patching
- Add a custom script in bin