base mechanics

404.md

@@ -0,0 +1,6 @@
+---
+title: Page Not Found
+search_exclude: true
+---  
+
+Sorry, but the page you were trying to view does not exist. Try searching for it or looking at the URL to see if it looks correct.

About-WorkflowHub.md

@@ -1,4 +1,6 @@
-# About WorkflowHub
+---
+title: About WorkflowHub
+---
 
 * [WorkflowHub](https://workflowhub.eu) is a new workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/).
 * WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics.

Gemfile

@@ -1,10 +1,4 @@
 source "https://rubygems.org"
 
-group :jekyll_plugins do
-  gem "github-pages"
-end
-
-group :test do
-  gem 'rake'
-  gem 'html-proofer'
-end
+# to publish on github page
+gem 'github-pages', group: :jekyll_plugins

How-to-find-and-retrieve-workflow(s)-from-WorkflowHub.md

@@ -1,4 +1,6 @@
-# How to find and retrieve workflow(s) from WorkflowHub?
+---
+title: How to find and retrieve workflow(s) from WorkflowHub?
+---
 
 ### How to search for workflows
 You can find and retrieve any workflow from WorkflowHub by:

How-to-make-a-workflow-RO-crate.md

@@ -1,4 +1,6 @@
-# How to make a workflow RO-crate?
+---
+title: How to make a workflow RO-crate?
+---
 
 More info about workflow RO-crate specification can be found in our [Workflow-RO-Crate](../Workflow-RO-Crate) section.
 

How-to-register-your-workflow(s)-in-WorkflowHub.md

@@ -1,4 +1,6 @@
-# How to register your workflow(s) in WorkflowHub?
+---
+tite: How to register your workflow(s) in WorkflowHub?
+---
 
 ### Prerequisites
 

How-to-register.md

@@ -1,4 +1,6 @@
-# How to register
+---
+title: How to register
+---
 
 > Which WorkflowHub instance?
 > * Use <https://dev.workflowhub.eu/> for testing - this testing instance may occasionally be wiped

Logging-in.md

@@ -1,4 +1,6 @@
-# How to log-in?
+---
+title: How to log-in?
+---
 
 Before you log in, you must have already [registered](../How-to-register) on WorkflowHub
 

Registering-a-workflow-with-a-diagram-and-abstract-CWL.md

@@ -1,5 +1,6 @@
-# **Simple** - Registering a workflow file with optionally a diagram and/or abstract-CWL
-
+---
+title: "**Simple** - Registering a workflow file with optionally a diagram and/or abstract-CWL"
+---
 
 ## Uploading or referencing the files
 

Registering-an-existing-Workflow-RO-Crate.md

@@ -1,4 +1,6 @@
-# **Advanced** - Registering a Workflow RO-Crate
+---
+title: "**Advanced** - Registering a Workflow RO-Crate"
+---
 
 Creating workflow RO-crates can be done using the [ro-crate-py ](https://github.com/ResearchObject/ro-crate-py) package. This gives you the advantage that you are not bound by the file limitations the workflow registration can give you. 
 

TRS.md

@@ -1,4 +1,6 @@
-# TRS API
+---
+title: TRS API
+---
 
 WorkflowHub implements GA4GH's [Tool Registry Service API](https://www.ga4gh.org/news/tool-registry-service-api-enabling-an-interoperable-library-of-genomics-analysis-tools/) to facilitate discovery of workflows in an interoperable way.
 

Updating-a-registered-workflow.md

@@ -1,4 +1,6 @@
-# Updating a registered workflow
+---
+title: Updating a registered workflow
+---
 
 
 ## Prerequisites

Workflow-RO-Crate/1.0/index.md

@@ -1,5 +1,6 @@
-# Workflow RO-Crate profile 1.0
-
+---
+title: Workflow RO-Crate profile 1.0
+---
 <!--  https://signposting.org/FAIR/  markup --->
 
 <link href="https://w3id.org/workflowhub/workflow-ro-crate/1.0" rel="cite-as" /> 
@@ -35,7 +36,7 @@
 <link href="http://schema.org/ImageObject" rel="item" />
 <link href="https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json" rel="item" />
 
-![Workflow RO-Crate](logo/ro-crate-workflow.svg)
+![Workflow RO-Crate](/assets/img/ro-crate-workflow.svg)
 
 * Authors:
   - Finn Bacall <https://orcid.org/0000-0002-0048-3300>

_config.yml

@@ -1,16 +1,21 @@
-theme: jekyll-theme-minimal
-markdown: CommonMarkGhPages
 title: WorkflowHub project
+
 email: [email protected]
 description: > # this means to ignore newlines until "baseurl:" 
   Project pages for developing and running WorkflowHub, 
   a registry of scientific workflows.
-baseurl: "" # the subpath of your site, e.g. /blog
-url: "https://about.workflowhub.eu" # the base hostname & protocol for your site
-github_username:  workflowhub-eu
-encoding: UTF-8
+
+remote_theme: ELIXIR-Belgium/[email protected]
 permalink: pretty
 
-logo: logo/workflowhub-square.svg
+defaults:
+  -
+    scope:
+      path: ""
+      type: "pages"
+    values:
+      layout: "page"
+      sidebar: main
 
-markdown: kramdown
+theme_variables: 
+  theme_color: 1f8787

_data/CONTRIBUTORS.yaml

@@ -0,0 +1,8 @@
+# List of contributors
+#
+# reference maintainers/contributors by their name used in contributors metadata section on the pages.
+
+Bert Droesbeke:
+    git: bedroesb
+    email: [email protected]
+    orcid: 0000-0003-0522-5674

_data/footer.yml

@@ -0,0 +1,26 @@
+copyright: "[workflowhub.eu](https://workflowhub.eu/) wiki content is distributed under [BSD 3-Clause 'New' or 'Revised' License](https://github.com/workflowhub-eu/about/blob/master/LICENSE), developed as part of [EOSC-Life](https://www.eosc-life.eu/), funded by European Union’s Horizon 2020 programme under grant agreement number [824087](https://cordis.europa.eu/project/id/824087)."
+extra_line: "workflowhub.eu lead development is part of [EOSC-Life](https://www.eosc-life.eu/), funded by European Union’s [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) programme under grant agreement [824087](https://cordis.europa.eu/project/id/824087)."
+columns:
+  - type: image
+    image_width: 120px
+    width: 3
+    src: '/assets/img/eosc-life.svg'
+    alt: EOSC-Life
+  - type: links
+    width: 3
+    children: 
+      - url_text: About us
+        url: /about_us.html
+      - url_text: Privacy
+        url: /privacy.html
+  - type: image
+    image_width: 88px
+    width: 3
+    src: '/assets/img/Flag_of_Europe.svg'
+    alt: European flag
+  - type: image
+    image_width: 120px
+    width: 3
+    src: '/assets/img/workflowhub_logo__square.svg'
+    alt: workflowhub logo square
+

_data/sidebars/main.yml

@@ -0,0 +1,26 @@
+subitems:
+  - title: Home
+    url: /index
+  - title: About
+    url: /What-is-WorkflowHub
+  - title: Workflow RO-crate
+    url: /Workflow-RO-Crate
+  - title: Registering
+    url: /how-to-register
+  - title: Logging in
+    url: /Logging-in
+  - title: Joining a project
+    url: /How-to-join-a-project
+  - title: Finding workflows
+    url: /How-to-find-and-retrieve-workflow%28s%29-from-WorkflowHub
+  - title: Making a RO-crate
+    url: /How-to-make-a-workflow-RO-crate
+  - title: Registering workflows
+    url: /How-to-register-your-workflow%28s%29-in-WorkflowHub
+    subitems:
+    - title: Existing Workflow RO-Crate
+      url: /Registering-an-existing-Workflow-RO-Crate
+    - title: Workflow + diagram and abstract CWL
+      url: /Registering-a-workflow-with-a-diagram-and-abstract-CWL
+    - title: Just a workflow
+      url: /Registering-just-a-workflow

_data/topnav.yml

@@ -0,0 +1,3 @@
+## Topnav single links
+## if you want to list an external url, use external_url instead of url. the theme will apply a different link base.
+subitems:

_sass/_bootstrap_variables.scss

@@ -0,0 +1,12 @@
+/*-----Theme colors-----*/
+$primary:       #1f8787;
+$secondary:     #f9b233;
+$light:         #f8f9fa;
+$blue:          #4a6eb3;
+$dark:          #212529;
+
+/*-----Custom values for Bootstrap variables-----*/
+$link-decoration: none;
+$nav-link-color: $dark;
+$nav-link-hover-color: $primary;
+$link-color: $blue;

_sass/_custom_classes.scss

@@ -0,0 +1,10 @@
+.navbar {
+    .navbar-brand {
+        font-size: 2.25rem;
+        padding-top: 0;
+        padding-bottom: 0;
+    }
+}
+img {
+    @extend .img-fluid;
+}

_sass/_custom_variables.scss

@@ -0,0 +1,71 @@
+/*-----General styling-----*/
+$font-family-theme: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", Arial, "Noto Sans", "Liberation Sans", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji" !default;
+$h2-color: $primary;
+
+/*-----Buttons hover style-----*/
+$btn-primary-bg-hover: $primary;
+$btn-primary-color-hover: $white;
+
+/*-----Top navigation-----*/
+$topnav-bg: $light;
+$topnav-title-color: $primary;
+$topnav-brand-height: 80px;
+$topnav-border: 0;
+
+/*-----Search-----*/
+$search-result-color: $primary;
+
+/*-----Sidebar-----*/
+$sidebar-bg: $light;
+$sidebar-color: $dark;
+$sidebar-lvl2-bg: $white;
+$sidebar-lvl2-color: $dark;
+$sidebar-lvl3-bg: $white;
+$sidebar-lvl3-color: $dark;
+$sidebar-bg-active: $primary;
+$sidebar-color-active: $white;
+
+/*-----TOC-----*/
+$toc-bg: $light;
+$toc-border: 0;
+
+/*-----Section navigation tiles-----*/
+$nav-card-bg: $white;
+$nav-card-header-bg: $dark;
+$nav-card-header-color: $white;
+$nav-card-badge-color: $body-color;
+$nav-card-badge-bg: $light;
+$nav-card-badge-color-hover: $white;
+$nav-card-badge-bg-hover: $primary;
+
+/*-----More information tiles-----*/
+$info-card-bg: $light;
+$info-card-header-bg: $dark;
+$info-card-header-color: $white;
+
+/*-----Contributors-cards-----*/
+$contr-card-bg: $light;
+
+/*-----Page contributors-----*/
+$contr-bg: $light;
+$contr-link-bg: $white;
+$contr-crown-bg: $dark;
+$contr-crown-color: $white;
+
+/*-----Events & news-----*/
+$news-title-bg: $primary;
+
+/*-----Default badge-----*/
+$badge-color: $body-color;
+$badge-bg: $light;
+$badge-color-hover: $white;
+$badge-bg-hover: $primary;
+
+/*-----Footer-----*/
+$footer-bg: $light;
+$footer-color: $dark;
+$footer-link-color: $dark;
+$footer-link-color-hover: $primary;
+$footer-copyright-bg: $gray-200;
+$footer-border: 0;
+