Welcome and Introductions

Overview

Teaching: 5 min
Exercises: 10 min
Questions
  • How will this workshop be run?

Objectives
  • Have access to all workshop related resources

Acknowledgement of Country

We pay our respect to the Aboriginal and Torres Strait Islander members of our community by acknowledging the traditional owners of the land on which we work and meet today. At Curtin University this is the Whadjuk people of the Nyungar Nation, and at Western Sydney University this is Darug, Eora, Dharawal (also referred to as Tharawal) and Wiradjuri people.

Requirements

Software

You will need the following software in order to benefit from this workshop:

We recommend that you also have Docker installed on your local machine, however this is not essential.

See the front page for links and instructions for NextFlow and Docker installs.

Hardware

You will need a personal laptop or desktop to work from. To run the workflows that we develop you can use one or more of the following:

Engagement

This workshop is developed for three main delivery methods:

  1. Facilitated, in person, at ICRAR-Curtin
  2. Facilitated, online, in parallel with (1)
  3. Self-paced, online, via this website.

For the workshop we have set up an Etherpad for people to contribute to as we go along. This means that contributions can be anonymous and asynchronous as needed. Whilst we have ADACS people here to facilitate the workshop, we encourage people to ask for help from their peers, and to offer help to those that may need it.

This workshop is all about learning by doing. We will be engaging in live coding type exercises for most of the workshop, and we will set challenges and exercises for you to complete in groups. The more you engage with your fellow learners and the more questions that you ask, the more that you will get out of this workshop.

We will be using sticky notes for in-person participants to indicate their readiness to move on: please stick them on your laptop screen to indicate if you need help or are done and ready to move ahead. For those joining online we’ll be using the cross or check icons (zoom) to indicate the same.

Conduct

This workshop will be an inclusive and equitable space, which respects:

We ask that you follow these guidelines:

Course structure

Day 1 (Users) 16th of Nov (Teams Link)

AWST AEDT Lesson
Before Before Pre-workshop survey
09:00 12:00 Welcome and Intro
    Workflows and Pipelines
    Introduction to Nextflow
    Nextflow Workflows
14:00 17:00 Finish

Day 2 (Developers) 23rd of Nov (Teams Link)

AWST AEDT Lesson
09:00 12:00 Nextflow Orchestration
    Containers
    Nextflow Best Practices
    Post-workshop Survey
14:00 17:00 END

On both days we’ll be taking breaks according to this plan

AWST AEDST Duration
10:00 13:00 10m
11:00 14:00 10m
12:00 15:00 30m
13:00 16:00 10m

Introduce yourselves

IceBreaker

Introduce yourself to your peers by telling us your name, a food that you would like to try but never have, and three words that describe your research interests.

Please also take some time to outline a workflow or task that you hope will benefit from this workshop.

Course content

Important links:

Key Points

  • Ask for help as soon as you need it