WORKSHOP: Unlocking nf-core - customising workflows for your research
Creators: name: Samaha, Georgina
name: Willet, Cali
name: Hakkaart, Chris
name: Beecroft, Sarah
name: Stott, Audrey
name: Ip, Alex
name: Cooke, Steele
Publisher: name: Zenodo
Year: 2023
Subjects: subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Workflows
subject: Nextflow
subject: nf-core
subject: http://edamontology.org/topic_0091
subject: http://edamontology.org/topic_0769

description: 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. <strong>Event description</strong> 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). <br> <strong>Materials</strong> 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. <strong>Materials shared elsewhere:</strong> 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
description: Roles: Lead trainers Dr Georgina Samaha, Dr Cali Willet, Dr Chris Hakkaart Facilitators: Dr Sarah Beecroft Infrastructure provision: Audrey Stott, Alex Ip, Steele Cooke