config.toml

# If deploy on github pages, change baseURL to repo's url
# eg: "https://USERNAME.github.io/" if this is your first website
# or "https://USERNAME.github.io/REPO_NAME/" if not the first
# replace USERNAME and REPO_NAME
# If deploy on Netlify, change it to "/"
baseURL = "/"
title = "systemPipe Workflow Environment"
ignoreFiles = ["\\.Rmd$", "\\.Rmarkdown$", "_cache$", "\\.knit", "\\.utf8"]
enableRobotsTXT = true
relativeURLs = true
# Hugo allows theme composition (and inheritance). The precedence is from left to right.
theme = ["docsy"]
# Will give values to .Lastmod etc.
enableGitInfo = true

# Language settings
contentDir = "content/en"
defaultContentLanguage = "en"
defaultContentLanguageInSubdir = false
# Useful when translating.
enableMissingTranslationPlaceholders = true

disableKinds = ["taxonomy", "taxonomyTerm"]

# Highlighting config
pygmentsCodeFences = false
pygmentsUseClasses = false
# Use the new Chroma Go highlighter in Hugo.
pygmentsUseClassic = false
pygmentsOptions = "linenos=table"
# See https://help.farbox.com/pygments.html
# pygmentsStyle = "vs"

# Configure how URLs look like per section.
[permalinks]
blog = "/:section/:year/:month/:day/:slug/"

## Configuration for BlackFriday markdown parser: https://github.com/russross/blackfriday
## not used in HUGO > 0.6
#[blackfriday]
#plainIDAnchors = true
#hrefTargetBlank = true
#angledQuotes = false
#latexDashes = true

# Image processing configuration.
[imaging]
resampleFilter = "CatmullRom"
quality = 75
anchor = "smart"

[services]
[services.googleAnalytics]
# Comment out the next line to disable GA tracking. Also disables the feature described in [params.ui.feedback].
id = "UA-158796879-1"

# Language configuration

[languages]
[languages.en]
title = "sysPipe"
description = "systemPipe Workflow Environment"
languageName ="English"
time_format_default = "2006-01-02"
time_format_blog = "2006-01-02"
## Weight used for sorting.
## uncomment below for more than one language support
#weight = 1
#[languages.no]
#title = "Goldydocs"
#description = "Docsy er operativsystem for skyen"
#languageName ="Norsk"
#contentDir = "content/no"
#time_format_default = "02.01.2006"
#time_format_blog = "02.01.2006"

[markup]
  [markup.goldmark]
    [markup.goldmark.renderer]
      unsafe = true
  ## markdown parse level, start with h2 headings ('##'), can be low as 1
  [markup.tableOfContents]
    endLevel = 6
    ordered = false
    startLevel = 1
#  [markup.highlight]
      # See a complete list of available styles at https://xyproto.github.io/splash/docs/all.html
      # Uncomment if you want your chosen highlight style used for code blocks without a specified language
      # guessSyntax = "true"

# Everything below this are Site Params

[params]
copyright = "The systemPipe Project"
#privacy_policy = "https://policies.google.com/privacy"

# First one is picked as the Twitter card image if not set on page.
# images = ["images/project-illustration.png"]



# A link to latest version of the docs. Used in the "version-banner" partial to
# point people to the main doc site.
url_latest_version = "https://github.com/systemPipeR/systemPipeR.github.io"

# Repository configuration (URLs for in-page links to opening issues and suggesting changes)
github_repo = "https://github.com/systemPipeR/systemPipeR.github.io"
# An optional link to a related project repo. For example, the sibling repository where your product code lives.
github_project_repo = "https://github.com/systemPipeR/systemPipeR.github.io"

# Since Github change default from "master" to "main", specify here.
github_branch = "main"
# Specify a value here if your content directory is not in your repo's root directory
# github_subdir = ""

# Google Custom Search Engine ID. Remove or comment out to disable search.
#gcs_engine_id = "68f09b43ef5dd93a4"

# Enable Algolia DocSearch
algolia_docsearch = false

# Enable Lunr.js offline search
offlineSearch = true

# Enable syntax highlighting and copy buttons on code blocks with Prism
prism_syntax_highlighting = true

# Menu title if your navbar has a versions selector to access old versions of your site.
# This menu appears only if you have at least one [params.versions] set.
version_menu = "v1.1dev"

# Flag used in the "version-banner" partial to decide whether to display a
# banner on every page indicating that this is an archived version of the docs.
# Set this flag to "true" if you want to display the banner.
archived_version = false

## The version number for the version of the docs represented in this doc set.
## Used in the "version-banner" partial to display a version number for the
## current doc set.
## uncomment below for more than one versions of website links
#version = "v1.0"

#[[params.versions]]
#  version = "v1.0"
#  githubbranch = "master"
#  url = "https://google.com"

#[[params.versions]]
#  version = "v1.1"
#  githubbranch = "master"
#  url = "https://google.com"

# User interface configuration
[params.ui]
# Enable to show the side bar menu in its compact state.
sidebar_menu_compact = false
#  Set to true to disable breadcrumb navigation.
breadcrumb_disable = false
#  Set to true to hide the sidebar search box (the top nav search box will still be displayed if search is enabled)
sidebar_search_disable = false
#  Set to false if you don't want to display a logo (/assets/icons/logo.svg) in the top nav bar
navbar_logo = true
# Set to true to disable the About link in the site footer
footer_about_disable = false

# Adds a H2 section titled "Feedback" to the bottom of each doc. The responses are sent to Google Analytics as events.
# This feature depends on [services.googleAnalytics] and will be disabled if "services.googleAnalytics.id" is not set.
# If you want this feature, but occasionally need to remove the "Feedback" section from a single page,
# add "hide_feedback: true" to the page's front matter.
[params.ui.feedback]
enable = false
# The responses that the user sees after clicking "yes" (the page was helpful) or "no" (the page was not helpful).
yes = 'Glad to hear it! Please <a href="https://github.com/systemPipeR/systemPipeR.github.io/issues/new">tell us how we can improve</a>.'
no = 'Sorry to hear that. Please <a href="https://github.com/systemPipeR/systemPipeR.github.io/issues/new">tell us how we can improve</a>.'

# Adds a reading time to the top of each doc.
# If you want this feature, but occasionally need to remove the Reading time from a single page,
# add "hide_readingtime: true" to the page's front matter
[params.ui.readingtime]
enable = false

[params.links]
# End user relevant links. These will show up on left side of footer and in the community page if you have one.
#[[params.links.user]]
#	name = "User mailing list"
#	url = "https://example.org/mail"
#	icon = "fa fa-envelope"
#        desc = "Discussion and help from your fellow users"
#[[params.links.user]]
#	name ="Twitter"
#	url = "https://example.org/twitter"
#	icon = "fab fa-twitter"
#        desc = "Follow us on Twitter to get the latest news!"
#[[params.links.user]]
#	name = "Stack Overflow"
#	url = "https://example.org/stack"
#	icon = "fab fa-stack-overflow"
#        desc = "Practical questions and curated answers"
# Developer relevant links. These will show up on right side of footer and in the community page if you have one.
[[params.links.developer]]
	name = "GitHub"
	url = "https://github.com/systemPipeR/"
	icon = "fab fa-github"
        desc = "View the source code"
[[params.links.developer]]
	name = "Bioconductor"
	url = "https://www.bioconductor.org/packages/release/bioc/html/systemPipeR.html"
	icon = "fa fa-dna"
        desc = "Find the stable release on Bioconductor"
[[params.links.developer]]
	name = "Find an issue?"
	url = "https://github.com/systemPipeR/systemPipeR/issues"
	icon = "fa fa-envelope"
        desc = "Discuss development issues around the project"


# Top-level navigation (horizontal)
## About
[[menu.main]]
  name = "About"
  weight = 1
  url = "/about/"
[[menu.main]]
  name = "Our Team"
  url = "/about/team/"
  parent = "About"
  weight = 1
[[menu.main]]
  name = "Publications"
  url = "/about/publications/"
  parent = "About"
  weight = 2
[[menu.main]]
  name = "Acknowledgement"
  url = "/about/acknowledgement/"
  parent = "About"
  weight = 3
[[menu.main]]
  name = "Contact"
  url = "/about/contact/"
  parent = "About"
  weight = 4
## SPR
[[menu.main]]
  name = "systemPipeR"
  weight = 2
  url = "/sp/"
  [[menu.main]]
    name = "systemPipeR Package"
    url = "/sp/spr/"
    parent = "systemPipeR"
    weight = 1
  [[menu.main]]
    name = "Introduction"
    url = "/sp/spr/introduction/"
    parent = "systemPipeR"
    weight = 2
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "Getting Started"
    url = "/sp/spr/gettingstarted/"
    parent = "systemPipeR"
    weight = 3
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "How to run a Workflow"
    url = "/sp/spr/sp_run/"
    parent = "systemPipeR"
    weight = 4
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "Workflow steps overview"
    url = "/sp/spr/steps/"
    parent = "systemPipeR"
    weight = 5
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "Workflow Templates"
    url = "/sp/spr/templates/"
    parent = "systemPipeR"
    weight = 6
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "CWL syntax"
    url = "/sp/spr/cwl/cwl_syntax/"
    parent = "systemPipeR"
    weight = 7
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPR and CWL"
    url = "/sp/spr/cwl/cwl_and_spr/"
    parent = "systemPipeR"
    weight = 8
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPR detailed installation"
    url = "/sp/spr/sprinstall/"
    parent = "systemPipeR"
    weight = 9
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "Reference Manual"
    url = "/sp/spr/spr_funcs/"
    parent = "systemPipeR"
    weight = 10
    [menu.main.params]
      level = 2
## SPTools
  [[menu.main]]
    name = "systemPipeRTools"
    weight = 10
    parent = "systemPipeR"
    url = "/sp/spt/"
  [[menu.main]]
    name = "Data Visualization"
    url = "/sp/spt/"
    parent = "systemPipeR"
    weight = 11
    [menu.main.params]
      level = 2
## SPRdata
  [[menu.main]]
    name = "systemPipeRdata"
    parent = "systemPipeR"
    url = "/sp/sprdata/"
    weight = 12
  [[menu.main]]
    name = "Vignette"
    url = "/sp/sprdata/systempiperdata/"
    parent = "systemPipeR"
    weight = 13
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "Rules"
    url = "/sp/sprdata/newwf/"
    parent = "systemPipeR"
    weight = 14
    [menu.main.params]
      level = 2
## SSPR Links
  [[menu.main]]
    name = "Links"
    url = "/spr/"
    parent = "systemPipeR"
    weight = 15
  [[menu.main]]
    name = "SPR Bioconductor"
    url = "http://bioconductor.org/packages/devel/bioc/html/systemPipeR.html"
    parent = "systemPipeR"
    weight = 16
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPR GitHub"
    url = "https://github.com/tgirke/systemPipeR"
    parent = "systemPipeR"
    weight = 17
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPRdata Bioconductor"
    url = "http://bioconductor.org/packages/devel/data/experiment/html/systemPipeRdata.html"
    parent = "systemPipeR"
    weight = 18
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPRdata GitHub"
    url = "https://github.com/tgirke/systemPipeRdata"
    parent = "systemPipeR"
    weight = 19
    [menu.main.params]
      level = 2
  [[menu.main]]
    name = "SPT GitHub"
    url = "https://github.com/tgirke/systemPipeTools"
    parent = "systemPipeR"
    weight = 20
    [menu.main.params]
      level = 2
## SPS
[[menu.main]]
  name = "Shiny"
  url = "/sps/"
  weight = 3
  [[menu.main]]
    name = "SPS Documentation"
    url = "/sps/"
    parent = "Shiny"
    weight = 1
  [[menu.main]]
    name = "Github"
    url = "https://github.com/systemPipeR/systemPipeShiny"
    parent = "Shiny"
    weight = 2
  [[menu.main]]
    name = "Bioconductor"
    url = "http://bioconductor.org/packages/3.13/bioc/html/systemPipeShiny.html"
    parent = "Shiny"
    weight = 3
## SPR workflows
[[menu.main]]
  name = "Workflows"
  url = "/spr_wf"
  weight = 4
  [[menu.main]]
    name = "Collection"
    url = "/spr_wf"
    parent = "Workflows"
    weight = 1
  [[menu.main]]
    name = "How to install Workflow"
    url = "/spr_wf/installwf/"
    parent = "Workflows"
    weight = 6
## Training
[[menu.main]]
  name = "Outreach"
  weight = 5
  url = "/outreach/"
[[menu.main]]
  name = "Conferences"
  url = "/outreach/conferences/"
  parent = "Outreach"
  weight = 1
[[menu.main]]
  name = "Presentations"
  url = "/outreach/presentations/"
  parent = "Outreach"
  weight = 2
[[menu.main]]
  name = "Videos Tutorials"
  url = "/outreach/videos/"
  parent = "Outreach"
  weight = 3
## News
[[menu.main]]
  name = "News"
  weight = 6
  url = "/News/"
[[menu.main]]
  name = "Bioconductor 3.12"
  url = "/news/release_3_12/"
  parent = "News"
  weight = 2
[[menu.main]]
  name = "Bioconductor 3.13"
  url = "/news/release_3_13/"
  parent = "News"
  weight = 1