update main from Dev

.github/workflows/jekyll.yml

@@ -1,10 +1,11 @@
-
 name: Jekyll site CI
 
 on:
+  push:
+    branches: [ main, master ]
   pull_request:
-    branches: [ master, main ]
-
+    branches: [ main, master ]
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -13,24 +14,23 @@ permissions:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
-
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch }}
 
       - name: Setup Ruby
-        uses: ruby/setup-ruby@v1.127.0
+        uses: ruby/setup-ruby@v1.204.0
         with:
-          ruby-version: '3.1'
+          ruby-version: '3.3'
           bundler-cache: true
           cache-version: 0
 
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v5
 
       - name: Install dependencies
         run: |
@@ -42,8 +42,30 @@ jobs:
           bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           PAGES_REPO_NWO: ${{ github.repository }}
-          JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
+          JEKYLL_ENV: production
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
+
+  deploy:
+    runs-on: ubuntu-24.04
+    needs: build
+
+    if: |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name)
+    concurrency:
+      group: "pages"
+      cancel-in-progress: true
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

Gemfile

@@ -0,0 +1,16 @@
+source "https://rubygems.org"
+
+gem "elixir-toolkit-theme-plugins", "~> 0.1.10"
+gem "webrick", "~> 1.8.1"
+gem "jekyll", "~> 4.3.2"
+gem "jemoji", "~> 0.13.0"
+gem "kramdown-parser-gfm", "~> 1.1"
+
+group :jekyll_plugins do
+  gem "jekyll-redirect-from", "~> 0.16.0"
+  gem "jekyll-sitemap", "~> 1.4"
+  gem "jekyll-github-metadata", "~> 2.16.0"
+  gem "jekyll-relative-links", "~> 0.7.0"
+  gem "jekyll-seo-tag", "~> 2.8"
+  gem "jekyll-remote-theme", "~> 0.4.3"
+end

README.md

@@ -1,6 +1,7 @@
 
 ## Acknowledgements
+To acknowledge your use of this service please follow [these instructions](/nextflow-seqera/main/acknowledgement)
 
-This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/) and the Queensland Government RICF programme. Bioplatforms Australia is funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
+This service forms part of the national [Australian BioCommons](https://www.biocommons.org.au/) infrastructure and is funded by Australian BioCommons and the Queensland Government RICF programme. Australian BioCommons is supported by [Bioplatforms Australia](https://bioplatforms.com/), which is funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
 
 This repository makes use of the ELIXIR toolkit theme: [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme). `assets/img/` content sourced from https://github.com/AustralianBioCommons/how-to-guides/

_config.yml

@@ -1,4 +1,4 @@
-title: "Aus Nextflow Seqera"
+title: "Australian Nextflow Seqera Service"
 description: A website for the Australian Nextflow Seqera service
 remote_theme: ELIXIR-Belgium/jekyll-bootstrap-theme@2.4.0
 topnav_title: Australian Nextflow Seqera Service
@@ -10,7 +10,6 @@ theme_variables:
     brand_logo: assets/img/Australian-Biocommons-Logo-Horizontal-RGB.png
   privacy_statement_url: https://www.biocommons.org.au/privacy
 
-
 defaults:
   -
     scope:

_data/CONTRIBUTORS.yml

@@ -16,7 +16,7 @@ Ziad Al-Bkhetan:
     git: ziadbkh
     email: ziad@biocommons.org.au
     orcid: 0000-0002-4032-5331
-    role: Service Owner
+    role: Product Manager
     affiliation: Australian BioCommons / University of Melbourne
 
 Johan Gustafsson:
@@ -26,4 +26,16 @@ Johan Gustafsson:
     role: Business analyst
     affiliation: Australian BioCommons / University of Melbourne
 
+Patrick Capon:
+    git: PatCapon39
+    email: patrick@biocommons.org.au
+    orcid: 000-0002-7396-5757
+    role: Editorial review
+    affiliation: Australian BioCommons / University of Melbourne
 
+Georgina Samaha:
+    git: georgiesamaha
+    email: georgina.samaha@sydney.edu.au
+    orcid: 0000-0003-0419-1476
+    role:
+    affiliation: Australian BioCommons / Sydney Informatics Hub at the University of Sydney

_data/affiliations.yml

@@ -11,7 +11,7 @@
 ### add new affiliations below as needed
 
 - name: Australian BioCommons
-  image_url: /assets/img/main_logo.png
+  image_url: /assets/img/Australian-Biocommons-Logo-Tagline-Infrastructure-RGB.png
   expose: true
   type: infrastructure
   url: https://www.biocommons.org.au/
@@ -33,6 +33,24 @@
   type: support
   url: https://www.biocommons.org.au/
 
+- name: Pawsey
+  image_url: /assets/img/pawsey-logo-beige.png
+  expose: true
+  type: support
+  url: https://pawsey.org.au/
+
+- name: NCI
+  image_url: /assets/img/NCI+Australia+logo+black+PNG+transparent.png
+  expose: true
+  type: support
+  url: https://nci.org.au/
+
+- name: Seqera
+  image_url: /assets/img/seqera_logo_color.png
+  expose: true
+  type: support
+  url: https://seqera.io/
+
 - name: Bioplatforms Australia
   image_url: /assets/img/bioplatforms-australia-logo.png
   expose: true
@@ -42,7 +60,7 @@
 - name: Australian Research Data Commons
   image_url: /assets/img/ARDC+logo+RGB.png
   expose: true
-  type: support
+  type: pilot
   url: https://ardc.edu.au/
 
 - name: NCRIS
@@ -51,32 +69,20 @@
   type: support
   url: https://www.education.gov.au/ncris
 
-- name: NCI
-  image_url: /assets/img/NCI+Australia+logo+black+PNG+transparent.png
-  expose: true
-  type: support
-  url: https://nci.org.au/
-
-- name: Pawsey
-  image_url: /assets/img/pawsey-logo-beige.png
-  expose: true
-  type: support
-  url: https://pawsey.org.au/
-
 - name: Queensland Cyber Infrastructure Foundation
   image_url: /assets/img/QCIF_Logo.png
   expose: true
-  type: support
+  type: pilot
   url: https://www.qcif.edu.au/
 
 - name: Melbourne Bioinformatics
   image_url: /assets/img/7465070.png
   expose: true
-  type: support
+  type: pilot
   url: https://mdhs.unimelb.edu.au/melbournebioinformatics
 
 - name: The University of Sydney
   image_url: /assets/img/Uni-logo-transparent.png
   expose: true
-  type: support
+  type: pilot
   url: https://www.sydney.edu.au/

_data/footer.yml

@@ -2,10 +2,15 @@
 copyright: This site uses Cookies. We use cookies to help the website run effectively. To find out more, read our [Privacy](https://www.biocommons.org.au/privacy) and [Cookie](https://www.biocommons.org.au/cookies) statements.
 extra_line:
 columns:
+  - type: image
+    image_width: 320px
+    width: 3
+    src: 'assets/img/Australian-Biocommons-Logo-Tagline-Infrastructure-RGB.png'
+    alt: Australian BioCommons logo featuring the tagline this service forms part of the national Australian BioCommons infrastructure
   - type: links
     width: 3
     children:
-      - url_text: Main
+      - url_text: Home
         url: /
       - url_text: Contributors
         url: /main/contributors

_data/sidebars/main.yml

@@ -1,22 +1,27 @@
-title: Main
+title: Home
 title_url: /
 subitems:
-  - title: Join the pilot project
-    url: /main/join_us
+  - title: Service Information
+    subitems:
+      - title: Service Terms
+        url: /main/service-terms
+      - title: Access Models
+        url: /main/access-models
+      - title: Acceptable Use
+        url: /main/acceptable-use
+      - title: Service Commitments
+        url: /main/service-commitments
+      - title: Privacy
+        url: /main/privacy
+      - title: Service History
+        url: /main/service-history
+  - title: Service Support
+    url: /main/support
+  - title: Service Acknowledgement
+    url: /main/acknowledgement
   - title: Contact us
-    url: /main/contact_us
+    url: /main/contact-us
   - title: Contributors
     url: /main/contributors
   - title: User Guide
     url: /user-guide/
-    subitems:
-      - title: Accessing the service
-        url: /user-guide/service-access
-      - title: Logging in
-        url: /user-guide/loggin
-      - title: Configure and use compute environments
-        url: /user-guide/compute-env
-      - title: Adding workflows
-        url: /user-guide/add-workflow
-      - title: Recommendations
-        url: /user-guide/hpc-recommendations

_data/sidebars/user-guide.yml

@@ -1,13 +1,24 @@
 title: User Guide
 title_url: /user-guide/
 subitems:
-  - title: Main
-    url: /
+  - title: User guide contents
+    subitems:
+      - title: Accessing the service
+        url: /user-guide/service-access
+      - title: Logging in
+        url: /user-guide/loggin
+      - title: Configure and use compute environments
+        url: /user-guide/compute-env
+      - title: Adding workflows
+        url: /user-guide/add-workflow
+      - title: Recommendations
+        url: /user-guide/hpc-recommendations
   - title: Contact us
-    url: /main/contact_us
+    url: /main/contact-us
   - title: Contributors
     url: /main/contributors
-
+  - title: Back to Home
+    url: /
 
 
-
+