Welcome and Introductions
Overview
Teaching: 5 min
Exercises: 10 minQuestions
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:
- MSTeams (if you are participating remotely)
- NextFlow
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:
- Your own laptop or PC
- Pawsey (e.g. Garrawarla or Setonix)
- OzStar
Engagement
This workshop is developed for three main delivery methods:
- Facilitated, in person, at ICRAR-Curtin
- Facilitated, online, in parallel with (1)
- 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:
- the lived experience of it’s attendees,
- the right for all to learn, and
- the fact that learning means making mistakes.
We ask that you follow these guidelines:
- Behave professionally. Harassment and sexist, racist, or exclusionary comments or jokes are not appropriate.
- All communication should be appropriate for a professional audience including people of many different backgrounds.
- Sexual or sexist language and imagery is not appropriate.
- Be considerate and respectful to others.
- Do not insult or put down other attendees.
- Critique ideas rather than individuals.
- Do not engage in tech-shaming.
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
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:
- Pre-Workshop survey
- Workshop website
- Workshop github
- Etherpad for discussions and sharing answers
- Post-Workshop survey
Key Points
Ask for help as soon as you need it