topics/{topic_name}/
├── metadata.yaml           # Topic config (name, type, editorial_board, subtopics)
├── images/                 # Shared images for all tutorials in this topic
├── faqs/                   # Topic-level FAQs
└── tutorials/
    └── {tutorial_name}/
        ├── tutorial.md         # Main tutorial content (required)
        ├── tutorial.bib        # BibTeX citations (optional)
        ├── slides.html         # Presentation slides (optional)
        ├── data-library.yaml   # Zenodo dataset definitions
        ├── workflows/
        │   ├── index.md        # layout: workflow-list
        │   ├── *.ga            # Galaxy workflow files (JSON)
        │   └── *-tests.yml     # Workflow test definitions
        └── faqs/               # Tutorial-specific FAQs
            └── index.md

---
name: "assembly"
type: "use"                    # "use" or "admin"
topic_type: technology         # technology, science, instructors, basics
title: "Assembly"
summary: "Description of the topic"
docker_image: "quay.io/galaxy/assembly-training"
edam_ontology: ["topic_0196"]
requirements:
  - type: "internal"
    topic_name: introduction
  - type: "internal"
    topic_name: sequence-analysis
    tutorials:
      - quality-control
editorial_board:
  - github-username
subtopics:
  - id: subtopic_id
    title: "Subtopic Title"
    description: "Description"

---
layout: tutorial_hands_on
title: "Tutorial Title"
zenodo_link: "https://zenodo.org/records/XXXXXXX"
questions:
  - "What biological question does this address?"
  - "How do we use tool X for task Y?"
objectives:
  - "Perform task X using Galaxy"
  - "Interpret output of tool Y"
time_estimation: "1H30M"
level: Introductory              # Introductory, Intermediate, Advanced
key_points:
  - "Take-home message 1"
  - "Take-home message 2"
contributions:
  authorship:
    - github-username
  editing:
    - github-username
  funding:
    - organization-id
  testing:
    - github-username
tags:
  - tag1
  - tag2
subtopic: subtopic_id           # Must match a subtopic id in topic metadata.yaml
edam_ontology:
  - topic_XXXX
requirements:
  - type: "internal"
    topic_name: introduction
    tutorials:
      - galaxy-intro-short
recordings:
  - youtube_id: VIDEO_ID
    length: 29M
    galaxy_version: "24.1"
    date: '2024-09-20'
follow_up_training:
  - type: "internal"
    topic_name: assembly
    tutorials:
      - assembly-decontamination
---

> <type-title>Title Text</type-title>
>
> Content here
>
{: .class_name}

> <agenda-title></agenda-title>
>
> In this tutorial, we will cover:
>
> 1. TOC
> {:toc}
>
{: .agenda}

> <hands-on-title>Descriptive Step Title</hands-on-title>
>
> 1. {% tool [Tool Display Name](toolshed.g2.bx.psu.edu/repos/owner/repo/tool_id/version) %} with the following parameters:
>    - {% icon param-file %} *"Input file"*: `dataset_name`
>    - {% icon param-select %} *"Parameter name"*: `Option value`
>    - {% icon param-text %} *"Text parameter"*: `some text`
>    - {% icon param-check %} *"Checkbox param"*: `Yes`
>
> 2. Examine the output file by clicking {% icon galaxy-eye %} (eye icon)
>
{: .hands_on}

> <question-title>Descriptive Question Title</question-title>
>
> 1. What is the N50 of the assembly?
> 2. How many contigs are there?
>
> > <solution-title></solution-title>
> >
> > 1. The N50 is 15 Mb
> > 2. There are 42 contigs
> >
> {: .solution}
>
{: .question}

> <comment-title>Optional Title</comment-title>
>
> Additional context or explanation that's helpful but not critical.
>
{: .comment}

> <tip-title>Helpful Tip Title</tip-title>
>
> A practical hint to help the learner.
>
{: .tip}

> <warning-title>Important Warning</warning-title>
>
> Something that could cause problems if ignored.
>
{: .warning}

> <details-title>Click to Expand</details-title>
>
> Extended information hidden by default. Good for background
> information that not all learners need.
>
{: .details}

> <code-in-title>Bash</code-in-title>
> ```bash
> echo "Hello Galaxy"
> ```
{: .code-in}

> <code-out-title>Output</code-out-title>
> ```
> Hello Galaxy
> ```
{: .code-out}

> > <code-in-title>Bash</code-in-title>
> > ```bash
> > command
> > ```
> {: .code-in}
>
> > <code-out-title>Output</code-out-title>
> > ```
> > output
> > ```
> {: .code-out}
{: .code-2col}

{% tool [Human-Readable Name](toolshed.g2.bx.psu.edu/repos/owner/repo/tool_id/version) %}
{% tool [Cut](Cut1) %}
{% tool [MultiQC](toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1) %}

{% icon galaxy-eye %}          # View/eye icon (inspect dataset)
{% icon galaxy-pencil %}       # Edit icon (edit attributes)
{% icon galaxy-delete %}       # Delete icon
{% icon galaxy-history %}      # History icon
{% icon tool %}                # Tool icon
{% icon question %}            # Question mark
{% icon congratulations %}     # Celebration

{% snippet faqs/galaxy/datasets_import_via_link.md %}
{% snippet faqs/galaxy/histories_create_new.md %}
{% snippet faqs/galaxy/datasets_rename.md %}
{% snippet faqs/galaxy/datasets_change_datatype.md datatype="fasta" %}
{% snippet faqs/galaxy/collections_build_list_paired.md %}

{% snippet faqs/galaxy/collections_build_list_paired.md datasets_description="the two Hi-C datasets (SRR7126301_1 and SRR7126301_2)" n="2" %}

{% snippet faqs/galaxy/histories_create_new.md box_type="hands_on" %}

{% snippet faqs/galaxy/workflows_run_trs.md path="topics/assembly/tutorials/my-tutorial/workflows/main_workflow.ga" title="My Workflow" %}

{% snippet faqs/galaxy/workflows_run_ds.md title="Genome profile analysis (WF1)" dockstore_id="github.com/iwc-workflows/kmer-profiling-hifi-VGP1/main" version="v0.6" %}

![Alt text for accessibility](../../images/image_name.png "Caption shown below figure")

@article{key2024,
  title={Article Title},
  author={Last, First and Other, Author},
  journal={Journal Name},
  year={2024},
  doi={10.xxxx/xxxxx}
}

{% cite key2024 %}

[Link text]({% link topics/topic_name/tutorials/tutorial_name/tutorial.md %})

Inline: $$ x^2 + y^2 = z^2 $$
Block (on its own line): $$ \sum_{i=1}^{n} x_i $$

| Column 1 | Column 2 | Column 3 |
|----------|----------|----------|
| data     | data     | data     |