_config.yml

# Welcome to Jekyll!
#
# This config file is meant for settings that affect your whole blog, values
# which you are expected to set up once and rarely edit after that. If you find
# yourself editing these this file very often, consider using Jekyll's data files
# feature for the data you need to update frequently.
#
# For technical reasons, this file is *NOT* reloaded automatically when you use
# 'bundle exec jekyll serve'. If you change this file, please restart the server process.

# Site settings
# These are used to personalize your new site. If you look in the HTML files,
# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
# You can create any custom variable you would like, and they will be accessible
# in the templates via {{ site.myvariable }}.
---
title: "Galaxy Training!"
email: EMAIL@gmail.com
description: A tutorial created by enthusiastic people on behalf of SIGU
url: "https://sigu-training.github.io/"
baseurl: "/clinical_genomics"
repository: sigu-training/clinical_genomics
repository_branch: "master"
gitter_url: "https://gitter.im/Galaxy-Training-Network/Lobby"
logo: "assets/images/GTN.png"
small_logo: "assets/images/GTN-60px.png"
help_url: https://help.galaxyproject.org/
other_languages: "fr, ja, es, pt, ar"
words_to_not_translate:
- bed
- dna
- expression
- downstream
- galaxy
- mapping
- reads
- rna
- single cell
- single-cell
- toolshed
- upstream
- wiggle
- workflow

# Where things are
source: .
destination: ./docs
plugins_dir: _plugins
layouts_dir: _layouts
data_dir: metadata
includes_dir: .

# Conversion
markdown: kramdown
highlighter: rouge
kramdown:
  input: GFM
  syntax_highlighter: rouge
  auto_ids: true
  toc_levels: 1..2

# Figure plugin parameters
figurify:
  skip_empty: true  # or false if you want to generate all figures, even those without any alt or title
  skip_layouts:
    - introduction_slides
    - tutorial_slides
    - base_slides
  skip_titles:
    - Example of an image with a caption

# Scholar
scholar:
  source: topics/
  bibliography: "**/*.bib"
  sort_by: "year,month"
  bibliography_template: bibtemplate
  style: _layouts/g3.csl

# Icon tag config
icon-tag:
  # in tutorials
  question: fa-question-circle
  solution: fa-eye
  hands_on: fa-pencil
  comment: fa-commenting-o
  tip: fa-lightbulb-o
  objectives: fa-bullseye
  requirements: fa-check-circle
  time: fa-hourglass-end
  keypoints: fa-key
  tool: fa-wrench
  workflow: fa-project-diagram
  feedback: fa-comments-o
  congratulations: fa-thumbs-up
  trophy: fa-trophy
  warning: fa-warning
  details: fa-info-circle
  exchange: fa-exchange
  wf-input: fa-chevron-circle-right
  sticky-note: fa-sticky-note
  new-history: fa-plus
  param-file: fa-file-o
  param-files: fa-files-o
  param-collection: fa-folder-o
  param-text: fa-pencil
  param-check: fa-check-square-o
  param-select: fa-filter
  param-repeat: fa-plus-square-o
  galaxy-eye: fa-eye
  galaxy-info: fa-info-circle
  galaxy-gear: fa-cog
  galaxy-history: fa-archive
  galaxy-library: fa-folder
  galaxy-pencil: fa-pencil
  galaxy-refresh: fa-refresh
  galaxy-barchart: fa-bar-chart
  galaxy-cross: fa-times
  galaxy-columns: fa-columns
  galaxy-tags: fa-tags
  galaxy-selector: fa-check-square-o
  galaxy-upload: fa fa-upload
  galaxy-chart-select-data: fa fa-database
  galaxy-save: fa fa-save
  galaxy-scratchbook: fa fa-th
  galaxy-dropdown: fa-caret-down
  workflow-runtime-toggle: fa-caret-square-o-up
  galaxy-wf-connection: fa-arrows-h
  galaxy-wf-new: fa-plus
  search: fa fa-search

  # menus, links
  zenodo_link: fa-files-o
  tutorial: fa-laptop
  slides: fa-slideshare
  interactive_tour: fa-magic
  workflow: fa-share-alt
  topic: fa-folder-o
  instances: fa-globe
  docker_image: fa-ship
  galaxy_instance: fa-external-link
  last_modification: fa-calendar
  references: fa-bookmark
  gitter: fa-comments
  help: fa-life-ring
  github: fa-github
  email: fa-envelope-o
  twitter: fa-twitter
  linkedin: fa-linkedin
  orcid: ai-orcid
  curriculum: fa-graduation-cap
  level: fa-graduation-cap
  hall-of-fame: fa-users

# To exclude in output (_site or docs)
exclude:
  - shared/font-awesome/src/
  - Gemfile
  - Gemfile.lock
  - package.json
  - package-lock.json
  - CONTRIBUTING.md
  - CONTRIBUTORS.yaml
  - LICENSE.md
  - README.md
  - Makefile
  - miniconda.sh
  - "**/README.md"
  - "**/*.yaml"
  - "**/*.yml"
  - "**/*.sh"
  - bin/
  - metadata/
  - templates/
  - vendor/
  - node_modules/
  - faq.md
  - 404.md

include:
  - .nojekyll

# Plugins
plugins:
  - jekyll-feed
  - jekyll-environment-variables
  - jekyll-github-metadata
  - jekyll-scholar
  - jekyll-redirect-from
  - jekyll-last-modified-at