Add Nextflow training collection

_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/

_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

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
+
+<div class="navigation-tiles row row-cols-1 row-cols-md-2 g-4 my-4">
+	<div class="col">
+		<a class="card h-100 text-decoration-none text-body" href="#self-paced-learning">
+			<div class="card-body">
+				<p class="card-title h2 border-0 pt-0">Self-paced learning</p>
+				<p class="card-text">Build your Nextflow skills through tutorials and practical learning resources.</p>
+			</div>
+		</a>
+	</div>
+	<div class="col">
+		<a class="card h-100 text-decoration-none text-body" href="#resources-for-trainers">
+			<div class="card-body">
+				<p class="card-title h2 border-0 pt-0">Resources for Trainers</p>
+				<p class="card-text">Find reusable workshop materials and guidance for delivering Nextflow training.</p>
+			</div>
+		</a>
+	</div>
+</div>
+
+{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %}
+
+## Self-paced learning
+
+<div class="row row-cols-1 row-cols-md-2 g-4 mb-5">
+	{% for resource in nextflow_resources %}
+		{% if resource.topics == "self-paced learning" %}
+			<div class="col">
+				<div class="card border h-100">
+					<div class="card-body d-flex flex-column">
+						<h3 class="card-title h5">{{ resource.name }}</h3>
+						<p class="card-text">{{ resource.description }}</p>
+						<dl class="mb-0 mt-auto small">
+							<dt>Provider</dt>
+							<dd>{{ resource.provider }}</dd>
+							<dt>Format</dt>
+							<dd>{{ resource.type }}</dd>
+						</dl>
+					</div>
+					<div class="card-footer bg-transparent">
+						 <a href="{{ resource.url }}" aria-label="Open {{ resource.name }}">Open resource</a>
+					</div>
+				</div>
+			</div>
+		{% endif %}
+	{% endfor %}
+</div>
+
+## Resources for trainers
+
+<div class="row row-cols-1 row-cols-md-2 g-4 mb-5">
+	{% for resource in nextflow_resources %}
+		{% if resource.topics == "workshop materials" %}
+			<div class="col">
+				<div class="card border h-100">
+					<div class="card-body d-flex flex-column">
+						<h3 class="card-title h5">{{ resource.name }}</h3>
+						<p class="card-text">{{ resource.description }}</p>
+						<dl class="mb-0 mt-auto small">
+							<dt>Provider</dt>
+							<dd>{{ resource.provider }}</dd>
+							<dt>Format</dt>
+							<dd>{{ resource.type }}</dd>
+						</dl>
+					</div>
+					<div class="card-footer bg-transparent">
+						 <a href="{{ resource.url }}" aria-label="Open {{ resource.name }}">Open resource</a>
+					</div>
+				</div>
+			</div>
+		{% endif %}
+	{% endfor %}
+</div>