From 5d0dc0ffe5d23735b19d44bebf487af36016caf6 Mon Sep 17 00:00:00 2001 From: GiorgiaMori Date: Fri, 28 Aug 2026 12:56:59 +1000 Subject: [PATCH 01/22] Update Nextflow collection --- pages/nextflow.md | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/pages/nextflow.md b/pages/nextflow.md index 8c872c8..2e8efb7 100644 --- a/pages/nextflow.md +++ b/pages/nextflow.md @@ -2,10 +2,19 @@ title: Nextflow type: Collection page_id: nextflow -datatable: true +datatable: false --- -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. +The Australian BioCommons and members of the [National Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative) have collaboratively developed high-quality Nextflow training resources over several years, 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 +
+ + Nextflow for the life sciences + + Unlocking nf-core: customising workflows for your research + + Using Containers in Nextflow + + Nextflow on HPC + +
\ No newline at end of file From 3ead31085d3cff475af6757b80a1cc2a7916718d Mon Sep 17 00:00:00 2001 From: GiorgiaMori Date: Fri, 28 Aug 2026 13:09:28 +1000 Subject: [PATCH 02/22] remove old Nextflow collection content --- _data/all_content_list.yml | 204 +------------------------------------ pages/nextflow.md | 1 - 2 files changed, 1 insertion(+), 204 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 7209bdc..13f13fa 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -571,206 +571,4 @@ provider: The Carpentries topics: online teaching 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 - 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 - 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://carpentries.org/blog/2020/03/tips-for-teaching-online/ \ No newline at end of file diff --git a/pages/nextflow.md b/pages/nextflow.md index 2e8efb7..d116c14 100644 --- a/pages/nextflow.md +++ b/pages/nextflow.md @@ -1,7 +1,6 @@ --- title: Nextflow type: Collection -page_id: nextflow datatable: false --- From 197fe238fa6186aa898f1ef97e872b2c8f2fe13a Mon Sep 17 00:00:00 2001 From: GiorgiaMori Date: Tue, 1 Sep 2026 10:57:37 +1000 Subject: [PATCH 03/22] update nextflow collection --- _data/all_content_list.yml | 34 +++++++++++++++++++++++++++++++++- pages/nextflow.md | 15 +++------------ 2 files changed, 36 insertions(+), 13 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 13f13fa..7f903d5 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -571,4 +571,36 @@ provider: The Carpentries topics: online teaching type: Blog - url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ \ No newline at end of file + url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ +- collection: + - nextflow + description: Introduction to Nextflow for life scientists, teaching the fundamentals of building and running reproducible analysis workflows through hands-on exercises. + name: Nextflow for the life sciences + provider: Sydney Informatics Hub and Australian BioCommons + topics: self-paced learning + type: Static website + url: https://zenodo.org/records/16791039 +- collection: + - nextflow + 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: Static website + url: https://zenodo.org/records/20453332 +- collection: + - nextflow + description: Practical examples on how to use 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: self-paced learning + type: YouTube video + url: https://zenodo.org/records/20740119 +- collection: + - nextflow + description: Introduction to configure and run Nextflow workflows on High Performance Computing (HPC) systems, including working with schedulers, software environments and Nextflow configuration. + name: Nextflow on HPC + provider: Australian BioCommons + topics: self-paced learning + type: static website + url: https://zenodo.org/records/17694728 diff --git a/pages/nextflow.md b/pages/nextflow.md index d116c14..be3ac98 100644 --- a/pages/nextflow.md +++ b/pages/nextflow.md @@ -1,19 +1,10 @@ --- title: Nextflow type: Collection -datatable: false +page_id: nextflow +datatable: true --- The Australian BioCommons and members of the [National Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative) have collaboratively developed high-quality Nextflow training resources over several years, 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. -
- - Nextflow for the life sciences - - Unlocking nf-core: customising workflows for your research - - Using Containers in Nextflow - - Nextflow on HPC - -
\ No newline at end of file +### Browse the collection \ No newline at end of file From 5b29ef97d9bf6a4c5e81334d0938d0fc1c9dbe05 Mon Sep 17 00:00:00 2001 From: GiorgiaMori Date: Tue, 1 Sep 2026 11:09:27 +1000 Subject: [PATCH 04/22] fix typos and add trainers package material --- _data/all_content_list.yml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 7f903d5..bf29259 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -578,15 +578,15 @@ name: Nextflow for the life sciences provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: Static website + type: static website url: https://zenodo.org/records/16791039 - collection: - nextflow - 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. + 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: Static website + type: static website url: https://zenodo.org/records/20453332 - collection: - nextflow @@ -600,7 +600,15 @@ - nextflow description: Introduction to configure and run Nextflow workflows on High Performance Computing (HPC) systems, including working with schedulers, software environments and Nextflow configuration. name: Nextflow on HPC - provider: Australian BioCommons + provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning type: static website url: https://zenodo.org/records/17694728 +- collection: + - nextflow + 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: static website + url: https://sydney-informatics-hub.github.io/nf4ls-materials/ From 3a5576b8cf88c3284c52086c55cfe4e28cf77290 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 1 Sep 2026 01:10:50 +0000 Subject: [PATCH 05/22] update library --- _data/all_content_list.yml | 218 ++++++++++++++++++++++++++++++++----- 1 file changed, 190 insertions(+), 28 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index bf29259..7209bdc 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -574,41 +574,203 @@ url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ - collection: - nextflow - description: Introduction to Nextflow for life scientists, teaching the fundamentals of building and running reproducible analysis workflows through hands-on exercises. - name: Nextflow for the life sciences - provider: Sydney Informatics Hub and Australian BioCommons - topics: self-paced learning - type: static website - url: https://zenodo.org/records/16791039 + 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: 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: static website - url: https://zenodo.org/records/20453332 + 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: Practical examples on how to use 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 + 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 provider: Australian BioCommons - topics: self-paced learning + 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://zenodo.org/records/20740119 + url: https://www.youtube.com/watch?v=I-hunuzsh6A&t=658s - collection: - nextflow - description: Introduction to configure and run 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: static website - url: https://zenodo.org/records/17694728 + 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 + type: YouTube video + url: https://www.youtube.com/watch?v=0xjc7PkF1Bc - collection: - nextflow - 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: static website - url: https://sydney-informatics-hub.github.io/nf4ls-materials/ + 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/ From f767a754238782ec2b756b8e36f2046cfd92c9ee Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 1 Sep 2026 01:22:01 +0000 Subject: [PATCH 06/22] update library --- _data/all_content_list.yml | 228 +++++++------------------------------ 1 file changed, 38 insertions(+), 190 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 7209bdc..fd2ff19 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -574,203 +574,51 @@ 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/ + description: Introduction to Nextflow for life scientists, teaching the fundamentals + of building and running reproducible analysis workflows through hands-on exercises. + name: Nextflow for the life sciences + provider: Sydney Informatics Hub and Australian BioCommons + topics: self-paced learning + type: static website + url: https://zenodo.org/records/16791039 - 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/ + 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: static website + url: https://zenodo.org/records/20453332 - 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 + description: Practical examples on how to use 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 + topics: self-paced learning type: YouTube video - url: https://www.youtube.com/watch?v=I-hunuzsh6A&t=658s + url: https://zenodo.org/records/20740119 - 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 - type: YouTube video - url: https://www.youtube.com/watch?v=0xjc7PkF1Bc + description: Introduction to configure and run 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: static website + url: https://zenodo.org/records/17694728 - 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/ + 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: static website + url: https://sydney-informatics-hub.github.io/nf4ls-materials/ From 36574450349e6946ae7f2f4d576fb0cf236e50b5 Mon Sep 17 00:00:00 2001 From: GiorgiaMori Date: Tue, 1 Sep 2026 16:04:27 +1000 Subject: [PATCH 07/22] update nextflow page cards --- _data/all_content_list.yml | 10 ++--- pages/nextflow.md | 77 ++++++++++++++++++++++++++++++++++++-- 2 files changed, 79 insertions(+), 8 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index fd2ff19..ab48ae4 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -579,7 +579,7 @@ name: Nextflow for the life sciences provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: static website + type: Static website url: https://zenodo.org/records/16791039 - collection: - nextflow @@ -589,7 +589,7 @@ name: 'Unlocking nf-core: Customising workflows for your research' provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: static website + type: Static website url: https://zenodo.org/records/20453332 - collection: - nextflow @@ -599,7 +599,7 @@ name: Using Containers in Nextflow provider: Australian BioCommons topics: self-paced learning - type: YouTube video + type: YouTube video and slides url: https://zenodo.org/records/20740119 - collection: - nextflow @@ -609,7 +609,7 @@ name: Nextflow on HPC provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: static website + type: Static website url: https://zenodo.org/records/17694728 - collection: - nextflow @@ -620,5 +620,5 @@ name: Nextflow for the life sciences workshop materials provider: Sydney Informatics Hub topics: workshop materials - type: static website + type: Static website url: https://sydney-informatics-hub.github.io/nf4ls-materials/ diff --git a/pages/nextflow.md b/pages/nextflow.md index be3ac98..4abb9a2 100644 --- a/pages/nextflow.md +++ b/pages/nextflow.md @@ -1,10 +1,81 @@ --- title: Nextflow type: Collection -page_id: nextflow -datatable: true --- The Australian BioCommons and members of the [National Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative) have collaboratively developed high-quality Nextflow training resources over several years, 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 \ No newline at end of file +### Browse the collection + +
+
+ +
+

Self-paced learning

+

Build your Nextflow skills through tutorials and practical learning resources.

+
+ +
+
+ +
+

Training materials

+

Find reusable workshop materials and guidance for delivering Nextflow training.

+
+ +
+
+ +{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow" %} + +## Self-paced learning + +
+ {% for resource in nextflow_resources %} + {% if resource.topics == "self-paced learning" %} +
+
+
+

{{ resource.name }}

+

{{ resource.description }}

+
+
Provider
+
{{ resource.provider }}
+
Format
+
{{ resource.type }}
+
+
+
+ Open resource +
+
+
+ {% endif %} + {% endfor %} +
+ +## Training materials + +
+ {% for resource in nextflow_resources %} + {% if resource.topics == "workshop materials" %} +
+
+
+

{{ resource.name }}

+

{{ resource.description }}

+
+
Provider
+
{{ resource.provider }}
+
Format
+
{{ resource.type }}
+
+
+
+ Open resource +
+
+
+ {% endif %} + {% endfor %} +
\ No newline at end of file From bc5d1b2a2fe7ddce65faf9a7c6edc39a6d60e88b Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 14 Sep 2026 14:38:00 +1000 Subject: [PATCH 08/22] Update Nextflow resources collection name --- pages/nextflow.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/nextflow.md b/pages/nextflow.md index 4abb9a2..ee14bde 100644 --- a/pages/nextflow.md +++ b/pages/nextflow.md @@ -26,7 +26,7 @@ The Australian BioCommons and members of the [National Bioinformatics Training C -{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow" %} +{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %} ## Self-paced learning @@ -78,4 +78,4 @@ The Australian BioCommons and members of the [National Bioinformatics Training C {% endif %} {% endfor %} - \ No newline at end of file + From 6037630be7322e8f80ff5958d69143c2e19c7e2e Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 14 Sep 2026 14:38:57 +1000 Subject: [PATCH 09/22] Rename Nextflow to Nextflow training in sidebar --- _data/sidebars/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From e761a028c2a6d2ee1a2b84f1dbf1b8b35bc91aec Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 14 Sep 2026 14:39:20 +1000 Subject: [PATCH 10/22] Rename nextflow.md to nextflow_training.md --- pages/{nextflow.md => nextflow_training.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pages/{nextflow.md => nextflow_training.md} (100%) diff --git a/pages/nextflow.md b/pages/nextflow_training.md similarity index 100% rename from pages/nextflow.md rename to pages/nextflow_training.md From 0ae63ede2f68b7864e7a3a93004831b02083e928 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 14 Sep 2026 04:40:20 +0000 Subject: [PATCH 11/22] update library --- _data/all_content_list.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index ab48ae4..2e54880 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -573,46 +573,46 @@ type: Blog url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ - collection: - - nextflow + - nextflow_training description: Introduction to Nextflow for life scientists, teaching the fundamentals of building and running reproducible analysis workflows through hands-on exercises. name: Nextflow for the life sciences provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: Static website + type: static website url: https://zenodo.org/records/16791039 - collection: - - nextflow + - 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: Static website + type: static website url: https://zenodo.org/records/20453332 - collection: - - nextflow + - nextflow_training description: Practical examples on how to use 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: self-paced learning - type: YouTube video and slides + type: YouTube video url: https://zenodo.org/records/20740119 - collection: - - nextflow + - nextflow_training description: Introduction to configure and run 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: Static website + type: static website url: https://zenodo.org/records/17694728 - collection: - - nextflow + - 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 @@ -620,5 +620,5 @@ name: Nextflow for the life sciences workshop materials provider: Sydney Informatics Hub topics: workshop materials - type: Static website + type: static website url: https://sydney-informatics-hub.github.io/nf4ls-materials/ From 7651cf83b5c5f3cd3294e2813a10d8fd0975dd03 Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 14 Sep 2026 14:41:39 +1000 Subject: [PATCH 12/22] Update title for Nextflow training resource --- pages/nextflow_training.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index ee14bde..a42d177 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -1,5 +1,5 @@ --- -title: Nextflow +title: Nextflow training type: Collection --- From 4a67d894e1d570ab692d725214c8bf3c1e20366d Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 17:56:20 +1000 Subject: [PATCH 13/22] Update pages/nextflow_training.md Co-authored-by: Melissa Burke <68895620+burkemlou@users.noreply.github.com> --- pages/nextflow_training.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index a42d177..f62b756 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -3,7 +3,7 @@ title: Nextflow training type: Collection --- -The Australian BioCommons and members of the [National Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative) have collaboratively developed high-quality Nextflow training resources over several years, 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. +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 From d31b6574e974ce7281e9ef50fbef5b876c2e496f Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 17:56:34 +1000 Subject: [PATCH 14/22] Update pages/nextflow_training.md Co-authored-by: Melissa Burke <68895620+burkemlou@users.noreply.github.com> --- pages/nextflow_training.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index f62b756..48e9c0e 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -55,7 +55,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo ## Training materials - +Find reusable workshop materials and guidance for delivering Nextflow training
{% for resource in nextflow_resources %} {% if resource.topics == "workshop materials" %} From e99ab525e8ab7602dfb6bed822eaa1eacf68a0b3 Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:09:56 +1000 Subject: [PATCH 15/22] Refactor Nextflow training page structure Updated headings and removed navigation tiles for better structure and clarity. --- pages/nextflow_training.md | 27 +++++---------------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index 48e9c0e..f988cae 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -7,28 +7,10 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo ### Browse the collection -
-
- -
-

Self-paced learning

-

Build your Nextflow skills through tutorials and practical learning resources.

-
- -
-
- -
-

Training materials

-

Find reusable workshop materials and guidance for delivering Nextflow training.

-
- -
-
- {% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %} -## Self-paced learning +#### Self-paced learning +##### Build your Nextflow skills through tutorials and practical learning resources
{% for resource in nextflow_resources %} @@ -54,8 +36,9 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo {% endfor %}
-## Training materials -Find reusable workshop materials and guidance for delivering Nextflow training +#### Resources for trainers +##### Find reusable workshop materials and guidance for delivering Nextflow training +
{% for resource in nextflow_resources %} {% if resource.topics == "workshop materials" %} From 18e7dc0483fe208137745eb59472c22fbe46bfb1 Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:12:35 +1000 Subject: [PATCH 16/22] Fix HTML div tags --- pages/nextflow_training.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index f988cae..bcfc52c 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -12,7 +12,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo #### Self-paced learning ##### Build your Nextflow skills through tutorials and practical learning resources -
+
{% for resource in nextflow_resources %} {% if resource.topics == "self-paced learning" %}
@@ -39,7 +39,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo #### Resources for trainers ##### Find reusable workshop materials and guidance for delivering Nextflow training -
+
{% for resource in nextflow_resources %} {% if resource.topics == "workshop materials" %}
From bfd476757f128ff4610fa8a371bde84e04429a15 Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:14:00 +1000 Subject: [PATCH 17/22] Enhance accessibility for resource links Updated resource links to include aria-label for accessibility. --- pages/nextflow_training.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index bcfc52c..e053c5e 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -12,7 +12,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo #### Self-paced learning ##### Build your Nextflow skills through tutorials and practical learning resources -
+
{% for resource in nextflow_resources %} {% if resource.topics == "self-paced learning" %}
@@ -28,7 +28,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo
- Open resource + Open resource
@@ -39,7 +39,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo #### Resources for trainers ##### Find reusable workshop materials and guidance for delivering Nextflow training -
+
{% for resource in nextflow_resources %} {% if resource.topics == "workshop materials" %}
@@ -55,7 +55,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo
- Open resource + Open resource
From 511052cc7baef81978d9e0f7b9d10ad1a9d4fd5b Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:17:13 +1000 Subject: [PATCH 18/22] Revise Nextflow training page structure and content Updated headings and added navigation tiles for self-paced learning and training materials. --- pages/nextflow_training.md | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index e053c5e..66b822c 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -5,12 +5,30 @@ 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 +## Browse the collection + +
+
+ +
+

Self-paced learning

+

Build your Nextflow skills through tutorials and practical learning resources.

+
+ +
+
+ +
+

Training materials

+

Find reusable workshop materials and guidance for delivering Nextflow training.

+
+ +
+
{% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %} -#### Self-paced learning -##### Build your Nextflow skills through tutorials and practical learning resources +### Self-paced learning
{% for resource in nextflow_resources %} @@ -36,8 +54,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo {% endfor %}
-#### Resources for trainers -##### Find reusable workshop materials and guidance for delivering Nextflow training +### Resources for trainers
{% for resource in nextflow_resources %} From 696e5bffbdfdc0043a25f148817e857329faf6e3 Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:20:08 +1000 Subject: [PATCH 19/22] Update training materials section to resources for trainers --- pages/nextflow_training.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index 66b822c..6d14b6a 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -17,9 +17,9 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo
- +
-

Training materials

+

Resources for Trainers

Find reusable workshop materials and guidance for delivering Nextflow training.

 From b1f2437236fdc1bba2bdb27bd6647be8b64a36ca Mon Sep 17 00:00:00 2001 From: Giorgia Mori <54341266+GiorgiaMori@users.noreply.github.com> Date: Mon, 28 Sep 2026 18:23:19 +1000 Subject: [PATCH 20/22] Change section headers from H2 to H3 --- pages/nextflow_training.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pages/nextflow_training.md b/pages/nextflow_training.md index 6d14b6a..41018f1 100644 --- a/pages/nextflow_training.md +++ b/pages/nextflow_training.md @@ -5,7 +5,7 @@ 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 +### Browse the collection
@@ -28,7 +28,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo {% assign nextflow_resources = site.data.all_content_list | add_collection | where: "collection", "nextflow_training" %} -### Self-paced learning +## Self-paced learning
{% for resource in nextflow_resources %} @@ -54,7 +54,7 @@ Nextflow is a powerful tool for scalable and reproducible bioinformatics workflo {% endfor %}
-### Resources for trainers +## Resources for trainers
{% for resource in nextflow_resources %} From b92c673d84edc8943380c39c9455980d9199b9ec Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 28 Sep 2026 08:23:56 +0000 Subject: [PATCH 21/22] update library --- _data/all_content_list.yml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index 2e54880..f102a7c 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -574,13 +574,13 @@ url: https://carpentries.org/blog/2020/03/tips-for-teaching-online/ - collection: - nextflow_training - description: Introduction to Nextflow for life scientists, teaching the fundamentals - of building and running reproducible analysis workflows through hands-on exercises. + 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: static website - url: https://zenodo.org/records/16791039 + 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 @@ -589,28 +589,28 @@ name: 'Unlocking nf-core: Customising workflows for your research' provider: Sydney Informatics Hub and Australian BioCommons topics: self-paced learning - type: static website - url: https://zenodo.org/records/20453332 + type: tutorial + url: https://sydney-informatics-hub.github.io/customising-nfcore-workshop-2026/ - collection: - nextflow_training - description: Practical examples on how to use existing containers with Nextflow - to create portable and reproducible workflows, including how to find suitable - container images and integrate them into Nextflow processes. + 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: self-paced learning type: YouTube video - url: https://zenodo.org/records/20740119 + url: youtube.com/watch?v=q4Rsq9QxEHk&feature=youtu.be - collection: - nextflow_training - description: Introduction to configure and run Nextflow workflows on High Performance - Computing (HPC) systems, including working with schedulers, software environments - and Nextflow configuration. + 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: static website - url: https://zenodo.org/records/17694728 + 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 @@ -620,5 +620,5 @@ name: Nextflow for the life sciences workshop materials provider: Sydney Informatics Hub topics: workshop materials - type: static website + type: trainer resources url: https://sydney-informatics-hub.github.io/nf4ls-materials/ From b95170790fac46ce93f1c3fb9775e246ff037d12 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 29 Sep 2026 01:37:42 +0000 Subject: [PATCH 22/22] update library --- _data/all_content_list.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_data/all_content_list.yml b/_data/all_content_list.yml index f102a7c..b77b31e 100644 --- a/_data/all_content_list.yml +++ b/_data/all_content_list.yml @@ -600,7 +600,7 @@ provider: Australian BioCommons topics: self-paced learning type: YouTube video - url: youtube.com/watch?v=q4Rsq9QxEHk&feature=youtu.be + url: 'https://www.youtube.com/watch?v=q4Rsq9QxEHk&feature=youtu.be ' - collection: - nextflow_training description: Introduction to configuring and running Nextflow workflows on High