type: map mapping:
name:
type: str
required: true
pattern: /^[a-z0-9_-]+$/
description: |
The internal identifier for a topic, it should be the same as the folder name.
_examples:
- epigenetics
- sequence-analysis
- admin
type:
type: str
required: true
enum:
- admin-dev
- basics
- data-science
- use
- instructors
description: |
The type of topic, some have subtly different behaviours.
`admin-dev`
: should be used for admin and developer topics that are not scientifically focused.
`basics`
: Only used for galaxy-interface type topics
`data-science`
: Topics which are not necessarily Galaxy focused but expand into broader communities
`use`
: These topics use galaxy for some analysis
`instructors`
: Specific to topics related to instruction of Galaxy
topic_type:
type: str
required: false
enum:
- technology
- field
description: |
These are used to organise the home page tutorials only, not used anywhere else.
title:
type: str
required: true
description: |
Title of the topic, this is displayed for users to see.
_examples:
- Proteomics
- Variant Analysis
summary:
type: str
required: true
description: |
A longer description of the contents of this topic
_examples:
- Statistical Analyses for omics data and machine learning using Galaxy tools
docker_image:
type: str
description: |
The image ID for an image which contains all of the tools and data for this topic.
_examples:
- quay.io/galaxy/sequence-analysis-training
subtopics:
type: seq
required: false
description: |
For large topics, we can define subtopics and create multiple tutorial lists, which separates the tutorials to help users find content that interests them more quickly.
sequence:
- type: map
mapping:
id:
type: str
required: true
pattern: /^[A-Za-z0-9_-]+$/
description: |
Subtopic ID, this should match what is used in tutorials.
_examples:
- single-cell
title:
type: str
required: true
description: |
Subtopic title, which is displayed for users to see.
_examples:
- Maintaining a Production Galaxy
- Single-cell RNA-seq
description:
type: str
required: true
description: |
A human readable textual description of a subtopic.
_examples: |
- "Start here if you are new to RNA-Seq analysis in Galaxy"
- "These tutorials take you from raw sequencing reads to pathway analysis"
- "Tutorials about analysis of single-cell RNA-seq data"
- "Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses"
enable:
type: bool
description: |
`false` to hide your topic from the production GTN. This is useful if you need a topic for a workshop, but have not finished making it up to GTN standards.
editorial_board:
type: seq
required: true
sequence:
- type: str
required: true
description: A contributor's ID in the CONTRIBUTORS.yaml file.
enum:
- CONTRIBUTORS
edam_ontology:
type: seq
sequence:
- type: str
pattern: /^topic_[0-9]+$/
description: |
An edam ontology id that describes the resource
_examples:
- topic_3173
requirements:
type: seq
description: List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to `follow_up_training`.
_examples:
- |
type: internal
topic_name: statistics
tutorials:
- age-prediction-with-ml
sequence:
- type: map
required: true
mapping:
type:
type: str
required: true
enum:
- internal
description: |
the type of link
topic_name:
type: str
description: |
The name of the topic
tutorials:
type: seq
sequence:
- type: str
description: |
List of required tutorials inside that topic
references:
type: seq
_examples: |
- |
authors: "Vaudel M, et al."
title: "Shedding light on black boxes in protein identification."
link: "https://www.ncbi.nlm.nih.gov/pubmed/24678044"
summary: "An extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics-for-proteomics. The material is completely based on freely available and open-source tools."
sequence:
- type: map
required: true
mapping:
authors:
type: str
required: true
title:
type: str
required: true
link:
type: str
required: true
summary:
type: str
gitter:
type: str
description: |
Link to a gitter channel that is more relevant for this topic than the default. E.g. a single cell topic, you could use `Galaxy-Training-Network/galaxy-single-cell` to link to their specific chat room in all of the child tutorials by default.
_examples:
- Galaxy-Training-Network/galaxy-single-cell
- galaxy-genome-annotation/Lobby
draft:
type: bool
description: |
`true` to hide your tutorial from the topic page (optional). This is useful if you need a tutorial for a workshop, but have not finished making it up to GTN standards.
tag_based:
type: bool
required: false
description: |
If this is a tag based topic (no tutorials of it's own)
then you must set this flag to indicate it as such, otherwise you
will find yourself with an empty topic page.
og_image:
type: str
description: |
A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter)
pattern: /^\/.*/
_examples:
- /assets/images/gat.png
custom_css:
type: str
description: |
Any custom CSS you might want to apply to a specific topic. This could be overriding e.g. the masthead colour (beware, will potentially conflict with themes.)
This is generally not a recommended property to set on topics, and something that is only used as part of outreach efforts to import content into the GTN.
_examples: |
- :root { --brand-color: red; }
logo:
type: str
description: |
A logo identifier (e.g. GTN) should be used by default, but may be swapped out for special logos from the assets folder.
logo_alt:
type: str
description: |
The alt text for the logo (MANDATORY).
learning_path_cta:
type: str
description: |
The specific learning path you wish to reference as a call-to-action for views who aren't sure where to get started.
It must be the name of a file in learning-pathways, without the `.md` suffix. This is not validated so, please make sure it's correct :)
_examples:
- intro-to-galaxy-and-genomics
- admin-training