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Authors: Hakkaart, Chris (orcid: 000... 

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Keywords: Workflows 

WORKSHOP: Hello Nextflow!

This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024.
Event description
The rise of big data has made it essential to be able to analyse and perform experiments on large...

Keywords: Bioinformatics, Workflows, Nextflow

WORKSHOP: Hello Nextflow! https://dresa.org.au/materials/workshop-hello-nextflow This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024. Event description The rise of big data has made it essential to be able to analyse and perform experiments on large datasets in a portable and reproducible manner. Nextflow is a popular bioinformatics workflow orchestrator that makes it easy to run data-intensive computational pipelines. It enables scalable and reproducible scientific workflows using software containers on any infrastructure. It allows the adaptation of workflows written in most languages and provides the ability to customise and optimise workflows for different computational environments, types and sizes of data. 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 scalable multi-step workflow. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.   Lead trainers:  Dr Chris Hakkaart, Developer Advocate, Seqera Labs. Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney. Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney. Facilitator: Dr Ziad Al Bkhetan, Australian BioCommons Infrastructure provision: Uwe Winter, Australian BioCommons Host: Dr Melissa Burke, Australian BioCommons   Training materials Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Materials shared elsewhere: The 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 (NCRIS via Bioplatforms Australia). Training materials webpage: https://sydney-informatics-hub.github.io/hello-nextflow/   Data and documentation:  https://github.com/Sydney-Informatics-Hub/hello-nextflow Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow
WORKSHOP: Unlocking nf-core - customising workflows for your research

This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.

Event description

Processing and analysing omics datasets poses many...

Keywords: Bioinformatics, Workflows, Nextflow, nf-core

WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research-1584ff39-e007-4422-9fd5-4e407df6b6c5 This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023. Event description Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community. nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals.  This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the nf-core/rnaseq workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment. This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).  Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).  https://sydney-informatics-hub.github.io/customising-nfcore-workshop Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, nf-core