rebranding the service

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 ELIXIR Belgium
+Copyright (c) 2023 Australian BioCommons
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,12 +1,6 @@
-## About
 
-Please see the [How-to Guide for the template](https://australianbiocommons.github.io/how-to-guide-template/) for more information on how to get started.  
-
-
-## Acknowledgements for the guides
+## Acknowledgements
 
 This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/), the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are 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)
-
-This template is based on the [ELIXIR Toolkit Theme example](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme-example).
+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

@@ -1,36 +1,48 @@
-title: How-to Guide
-# This appears in the html browser tab for the site title (seen mostly by search engines, not users)
-
-#topnav_title: Website title
-# Optional: this appears on the top navigation bar next to the main_logo.svg icon
-
-description: "A bioinformatics focused How-to Guide"
-# Metadata description of the website
-
-remote_theme: ELIXIR-Belgium/[email protected]
+title: "Aus Nextflow Seqera"
+description: A website for the the Australian Nextflow Seqera service
+remote_theme: ELIXIR-Belgium/[email protected]
+topnav_title: Aus Nextflow Seqera
 
 theme_variables:
   # biocommons blue
   theme_color: 205a86
   topnav:
-    brand_logo: assets/img/logo_example.png
+    brand_logo: assets/img/main_logo.png
+  privacy_statement_url: https://www.biocommons.org.au/privacy
+
+permalink: /:categories/:year/:month/:day/:title
 
 exclude:
   - README.md
+  - .gitignore
+  - var/
   - vendor
+  - Gemfile*
+  - LICENSE
+
+permalink: /:categories/:year/:month/:day/:title
 
 defaults:
   -
     scope:
       path: ""
       type: "pages"
     values:
-      permalink: /:basename
       layout: "page"
       sidebar: main
-
+  -
+    scope:
+      path: "user-guide"
+      type: "pages"
+    values:
+      sidebar: user-guide
+
+
 plugins:
-  - jemoji
+  - elixir-toolkit-theme-plugins
+  - jekyll-redirect-from
+  - jekyll-seo-tag
   - jekyll-sitemap
   - jekyll-github-metadata
-  - webrick
+  - jemoji
+  - webrick

_data/CONTRIBUTORS.yml

@@ -12,11 +12,18 @@
 # an example contributor is included below
 # example roles include "lead", "first-author", "author", "editor", "workflow-tester"
 
-#Johan Gustafsson:
-#    git: supernord
-#    email: [email protected]
-#    orcid: 0000-0002-2977-5032
-#    role: author
-#    affiliation: Australian BioCommons / University of Melbourne
+Ziad Al-Bkhetan:
+    git: ziadbkh
+    email: [email protected]
+    orcid: 0000-0002-4032-5331
+    role: Service Owner
+    affiliation: Australian BioCommons / University of Melbourne
+
+Johan Gustafsson:
+    git: supernord
+    email: [email protected]
+    orcid: 0000-0002-2977-5032
+    role: Business analyst
+    affiliation: Australian BioCommons / University of Melbourne
 
 

_data/footer.yml

@@ -1,11 +1,11 @@
 # see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml
 copyright: Copyright notice
-extra_line: Add other relevant information here!
+extra_line:
 columns:
   - type: links
     width: 3
     children:
-      - url_text: Home
+      - url_text: Main
         url: /
       - url_text: Contributors
-        url: /contributors
+        url: /main/contributors

_data/sidebars/main.yml

@@ -1,14 +1,12 @@
+title: Main
+title_url: /
 subitems:
-  - title: About
-    url: /index
-  - title: Standard example page
-    url: /example_page
-  - title: Workflow How-to Guide example pages
-    subitems:
-      - title: Example workflow guide page
-        url: /example_bioinformatics_workflow_page
-      - title: Example workflow documentation page
-        url: /example_workflow_documentation_page
+  - title: Join the pilot project
+    url: /main/join_us
+  - title: Contact us
+    url: /main/contact_us
   - title: Contributors
-    url: /contributors
+    url: /main/contributors
+  - title: User Guide
+    url: /user-guide/
 

_data/sidebars/user-guide.yml

@@ -0,0 +1,13 @@
+title: User Guide
+title_url: /user-guide/
+subitems:
+  - title: Main
+    url: /
+  - title: Contact us
+    url: /main/contact_us
+  - title: Contributors
+    url: /main/contributors
+
+
+
+

_data/topnav.yml

@@ -1,6 +1,8 @@
 ## 
 ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base.
 subitems:
-- title: About
-  url: /index
-
+- title: Home
+  url: /
+
+- title: User Guide
+  url: /user-guide

_sass/_bootstrap_variables.scss

@@ -12,7 +12,7 @@ $bioc-green: #2cb77c;
 
 /*-----Theme colors-----*/
 $primary:       $bioc-blue;
-$secondary:     $bioc-green;
+$secondary:     $bioc-teal;
 $light:         #f8f9fa;
 $blue:          $bioc-blue;
 $dark:          #212529;

index.md

@@ -1,36 +1,63 @@
 ---
-title: How-to Guide landing page template
-type: template
-contributors: 
-description: Add a plain text description here.
-affiliations: 
+title: The Australian Nextflow Seqera Service
+toc: false
 ---
 
 
-## About 
+## Project outline
 
-> Add 2-3 sentences here explaining the purpose of the specific guide you are creating.
+Through a licence agreement with Seqera Labs, Australian BioCommons is in the process of standing up a national Nextflow Seqera service, enabling a centralised command post for Nextflow pipelines to be offered as a fully subsidised service for Australian researchers.
 
+Working with partners including service hosts Pawsey Supercomputing Research Centre, NCI, SIH, QCIF and Melbourne Bioinformatics, the Australian Nextflow Seqera Service will deliver a key component of BioCommon’s vision for an ecosystem of data analysis and digital asset stewardship platforms. The project is delivered through the BioCommons ‘Bring Your Own Data’ Project, which attracts ARDC and Bioplatforms Australia funding.
 
-## Guide sections
+## Aims of the pilot project
 
-> You can use this section to add navigation tiles for the pages you have created as part of your guide.
+The pilot project has three key ambitions, which are to
 
+1. Establish a service where BioCommons early adopters, including both science and method communities, can easily run, manage and monitor the execution of Nextflow workflows on dedicated compute infrastructure.
 
-## Please cite this guide as follows
+2. Understand service demand and utilisation by working with BioCommons communities and assessing interest from other communities
 
-> [Citation information goes here]
+3. Develop service operational models; understand costs and benefits; develop a business case for continuing the service
 
+At the end of the pilot phase, the Australian BioCommons will make the decision on providing this service for a long term. This depends on the feedback and outcomes of this pilot project. Successful use cases will play a major role in influencing the decision.
 
-## Acknowledgements
+## Service status
 
-> Don't delete anything from this section, only add.
+Since investigations commenced in July 2022:
 
-This guide makes use of the [ELIXIR toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+- Nextflow Seqera has been deployed on Pawsey infrastructure
 
-{% include image.html file="elixir-toolkit-theme_logo.svg" alt="Elixir Toolkit Theme logo" max-width="15em" %}
+- Researchers at AGRF, AusARG, UNSW and the University of Sydney are developing and running Nextflow pipelines to test the service
 
-## References
+- Test pipelines have been run on Pawsey, NCI, AGRF and AWS infrastructure.
 
-> Add references as needed.
- 
+- Research infrastructure teams at QUT and St Vincent’s institute medical research are exploring the use of the service
+
+ <br />
+
+## Quick access links
+
+[Join the pilot project](/nextflow-seqera/main/join_us){: class="btn btn-primary col-3"}
+
+<br />  
+
+<br />  
+
+<br />  
+
+
+<div class="text-center">
+    <div class="row">
+        <div class="col"><img src="assets/img/bioplatforms-australia-logo.png" class="rounded col-4" alt="bioplatforms australia" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/ARDC+logo+RGB.png" class="rounded col-4" alt="Australian Research Data Commons" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/ncris-logo1.png" class="rounded col-4" alt="NCRIS" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/pawsey-logo-beige.png" class="rounded col-4" alt="Pawsey Supercomputing Centre" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+    </div>
+    <div class="row">
+        <div class="col"><img src="assets/img/NCI+Australia+logo+black+PNG+transparent.png" class="rounded col-4" alt="National Computational Infrastructure (NCI)" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/QCIF_Logo.png" class="rounded col-4" alt="Queensland Cyber Infrastructure Foundation" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/7465070.png" class="rounded col-4" alt="Melbourne Bioinformatics" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+        <div class="col"><img src="assets/img/Uni-logo-transparent.png" class="rounded col-4" alt="The University of Sydney" style="width:225px; height:100px; padding: 10px 10px 10px 10px;"></div>
+    </div>
+</div>