diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 7209bdc..b77b31e 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -573,204 +573,52 @@ type: Blog url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ - collection: - - nextflow - description: 'This workshop will provide you with the foundational knowledge required - to build Nextflow workflows. ' - name: Hello Nextflow (SIH) - provider: Sydney Informatics Hub (SIH) - topics: nextflow pipelines, nextflow workflows - type: self-paced tutorial and workshop - url: https://sydney-informatics-hub.github.io/hello-nextflow/ -- collection: - - nextflow - description: An How-To Guide to aid beginners in developing their own Nextflow workflows - from a template-nf. - name: Template-nf user guide - provider: Sydney Informatics Hub (SIH) - topics: nextflow template - type: How-to Guide - url: https://sydney-informatics-hub.github.io/template-nf-guide/ -- collection: - - nextflow - description: 'Get started by installing Nextflow, setting up a development environment - with the Nextflow VS Code extension, and running your first script. ' - name: Nextflow Docs - provider: Nextflow - topics: getting started, running and developing pipelines, software dependencies, - compute and storage - type: Documentation - url: https://www.nextflow.io/docs/latest/index.html -- collection: - - nextflow - description: A collection of learning resources and Nextflow tutorials. - name: Nextflow community training portal - provider: Nextflow - topics: nextflow training - type: self-paced tutorial, interactive exercises - url: https://training.nextflow.io/ -- collection: - - nextflow - description: Nextflow webpage - name: Nextflow Homepage - provider: Nextflow - topics: documentation, training, resources and Forums - type: Webpage - url: https://nextflow.io/ -- collection: - - nextflow - description: Nextflow YouTube channel - name: Nextflow YouTube channel - provider: YouTube - topics: videos and podcasts - type: YouTube channel - url: https://www.youtube.com/c/Nextflow -- collection: - - nextflow - description: This workshop will provide you with the foundational knowledge required - to run and customise nf-core workflows in a reproducible manner. - name: Reproducible workflows with nf-core - provider: Sydney Informatics Hub (SIH) - topics: nf-core - type: self-paced tutorial and workshop - url: https://sydney-informatics-hub.github.io/customising-nfcore-workshop/ -- collection: - - nextflow - description: A lesson that motivates the use of Nextflow and nf-core as development - tools for building and sharing reproducible data science workflows. - name: Introduction to Bioinformatics workflows with Nextflow and nf-core - provider: 'The Carpentries ' - topics: nextflow, nf-core - type: self-paced tutorial - url: https://carpentries-incubator.github.io/workflows-nextflow/index.html -- collection: - - nextflow - description: This tutorial shows how convert the basic rnaseq-nf pipeline to Nextflow - DSL-2. - name: nfcamp-tutorial - provider: GitHub - topics: nf-core, DSL-2 - type: self-paced tutorial - url: https://github.com/nextflow-io/nfcamp-tutorial -- collection: - - nextflow - description: This blog post describes how to build analytical pipelines using version - 2 of the DSL (domain specific language) that the Nextflow workflow manager implements. - name: Building a DSL2 pipeline in Nextflow - provider: Anthony Underwood (Author) - topics: nf-core, DSL-2 - type: blog post - url: https://antunderwood.gitlab.io/bioinformant-blog/posts/building_a_dsl2_pipeline_in_nextflow/ -- collection: - - nextflow - description: "A global community effort to collect a curated set of open\u2011source\ - \ analysis pipelines built using Nextflow." - name: nf-core Homepage - provider: nf-core - topics: nf-core - type: Webpage - url: https://nf-co.re/ -- collection: - - nextflow - description: 'This page collects some recurring implementation patterns used in - Nextflow applications. ' - name: Nextflow Patterns - provider: Nextflow - topics: nextflow implementation patterns - type: self-paced tutorial - url: https://nextflow-io.github.io/patterns/ -- collection: - - nextflow - description: Introductory training on Nextflow - name: Nextflow Training - provider: Curtin Institute of Radio Astronomy (CIRA), The Carpentries - topics: workflows, pipelines, best practices - type: self-paced tutorial - url: https://carpentries-incubator.github.io/Pipeline_Training_with_Nextflow/ -- collection: - - nextflow - description: Launch an nf-core pipeline on Gadi - name: nf-core NCI Gadi HPC Configuration - provider: nf-core - topics: nf-core, HPC configuration - type: self-paced tutorial - url: https://nf-co.re/configs/nci_gadi/ -- collection: - - nextflow - description: Launch an nf-core pipeline on Setonix - name: nf-core Pawsey Setonix HPC Configuration - provider: nf-core - topics: nf-core, HPC configuration - type: self-paced tutorial - url: https://nf-co.re/configs/pawsey_setonix/ -- collection: - - nextflow - description: "A section of Seqera Labs\u2019 blog dedicated to articles about Nextflow,\ - \ a platform to share updates, tutorials, community stories, and advancements\ - \ related to Nextflow." - name: The Open Science Blog - provider: Seqera - topics: seqera, nexftlow - type: Blog - url: https://seqera.io/blog/tag-nextflow/ -- collection: - - nextflow - description: The Australian BioCommons Seqera Nextflow Service webpage, providing - an overview of the service, its features, benefits, access information, and relevant - resources for researchers interested in using Nextflow for bioinformatics workflows. - name: The Australian Nextflow Seqera Service + - nextflow_training + description: 'A hands-on introduction to Nextflow for life scientists, including + the fundamentals of building and running reproducible analysis workflows. ' + name: Nextflow for the life sciences + provider: Sydney Informatics Hub and Australian BioCommons + topics: self-paced learning + type: tutorial + url: http://sydney-informatics-hub.github.io/hello-nextflow-2025/ +- collection: + - nextflow_training + description: Introduction to adapting existing nf-core workflows to suit your research + needs, how to configure, customise and extend pipelines without having to build + workflows from scratch. + name: 'Unlocking nf-core: Customising workflows for your research' + provider: Sydney Informatics Hub and Australian BioCommons + topics: self-paced learning + type: tutorial + url: https://sydney-informatics-hub.github.io/customising-nfcore-workshop-2026/ +- collection: + - nextflow_training + description: Practical examples of using existing containers with Nextflow to create + portable and reproducible workflows, including how to find suitable container + images and integrate them into Nextflow processes. + name: Using Containers in Nextflow provider: Australian BioCommons - topics: seqera, nexftlow - type: Webpage - url: https://www.biocommons.org.au/seqera-service -- collection: - - nextflow - description: Recording focused on Nextflow DSL2, explaining how to use modules to - build more scalable, maintainable, and reusable bioinformatics workflows. It covers - key DSL2 concepts, structuring pipelines with modules, and best practices for - workflow development using nf-core standards. - name: DSL2 and Modules - Nextflow Workshop 2022 - provider: Nextflow - topics: DSL-2, nextflow, nf-core - type: YouTube video - url: https://www.youtube.com/watch?v=6k9lWewSBYc -- collection: - - nextflow - description: "Discussion about the advancements in Nextflow\u2019s Domain Specific\ - \ Language version 2 (DSL2). It covers topics such as the modularization of workflows,\ - \ enhanced code reusability, and the integration of community-driven modules,\ - \ aiming to provide viewers with a comprehensive understanding of DSL2\u2019s\ - \ capabilities and its application in building complex, maintainable bioinformatics\ - \ pipelines." - name: Introduction to DSL2 in Nextflow - provider: nf-core - topics: DSL-2, nextflow - type: YouTube video - url: https://www.youtube.com/watch?v=I-hunuzsh6A&t=658s -- collection: - - nextflow - description: 'A video to provide HPC users with an overview on how to develop new - and redevelop existing workflows using not only Nextflow but also industry accepted - best practices, including code modularity and reuse, rapid prototyping and deployment, - and platform independence. ' - name: 'Introduction to Nextflow for Data Intensive Pipelines: Part 1' - provider: Pawsey Supercomputing Research Centre - topics: nextflow - type: YouTube video - url: https://www.youtube.com/watch?v=bIRLbYPWHoM -- collection: - - nextflow - description: A detailed walkthrough of the pipeline code structure for the new DSL2 - template in Nextflow. - name: 'DSL2: Pipeline Structure Walkthrough' - provider: nf-core - topics: DSL-2, nextflow + topics: self-paced learning type: YouTube video - url: https://www.youtube.com/watch?v=0xjc7PkF1Bc -- collection: - - nextflow - description: This is a workshop for those who are completely new to Nextflow - name: Hello Nextflow (Nextflow) - provider: Nextflow - topics: nextflow - type: self-paced tutorial - url: https://training.nextflow.io/hello_nextflow/ + url: 'https://www.youtube.com/watch?v=q4Rsq9QxEHk&feature=youtu.be ' +- collection: + - nextflow_training + description: Introduction to configuring and running Nextflow workflows on High + Performance Computing (HPC) systems, including working with schedulers, software + environments and Nextflow configuration. + name: Nextflow on HPC + provider: Sydney Informatics Hub and Australian BioCommons + topics: self-paced learning + type: tutorial + url: 'https://sydney-informatics-hub.github.io/nextflow-hpc-workshop/ ' +- collection: + - nextflow_training + description: Nextflow for the Life Sciences Trainer package that brings together + ready-to-reuse teaching materials, instructor guidance and hands-on exercises, + making it easier for trainers to adapt and deliver Nextflow training for their + own communities. + name: Nextflow for the life sciences workshop materials + provider: Sydney Informatics Hub + topics: workshop materials + type: trainer resources + url: https://sydney-informatics-hub.github.io/nf4ls-materials/ diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index f1c2e41..402ad8b 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -11,8 +11,8 @@ subitems: url: /structural_biology - title: Skills for Trainers url: /skills_for_trainers - - title: Nextflow - url: /nextflow + - title: Nextflow training + url: /nextflow_training - title: About url: /about - title: Contact us diff --git a/pages/nextflow.md b/pages/nextflow.md deleted file mode 100644 index 8c872c8..0000000 --- a/pages/nextflow.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: Nextflow -type: Collection -page_id: nextflow -datatable: true ---- - -Nextflow has become a powerful tool for scalable and reproducible bioinformatics workflows, and nf-core provides a rich ecosystem of curated pipelines built on Nextflow’s latest framework. -The Nextflow collection is curated and endorsed by Australian BioCommons and is designed to support individuals interested in navigating the Nextflow ecosystem. The collection consists of tutorials, workshops, recorded talks, blogs, and key websites. These resources cover fundamental concepts, best practices, and advanced topics to support your journey in workflow development and automation. - -### Browse the collection diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md new file mode 100644 index 0000000..41018f1 --- /dev/null +++ b/pages/nextflow_training.md @@ -0,0 +1,81 @@ +--- +title: Nextflow training +type: Collection +--- + +Nextflow is a powerful tool for scalable and reproducible bioinformatics workflows, and nf-core provides a rich ecosystem of curated pipelines built on Nextflow’s latest framework. Australian BioCommons and the [National Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative) have collaboratively developed high-quality Nextflow training resources, supporting life science researchers across Australia to build practical workflow skills. This collection brings these materials together in one place for self-paced learning and for trainers who want to reuse and rerun workshops in their local context. + +### Browse the collection + +
+ +{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %} + +## Self-paced learning + +{{ resource.description }}
+{{ resource.description }}
+