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Merge branch 'galaxyproject:main' into cross-post
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@kkamieniecka
kkamieniecka authored Oct 5, 2023
2 parents cff7c0e + 900e472 commit 60d2ee2
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2 changes: 2 additions & 0 deletions .github/workflows/ci-main.yml
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Expand Up @@ -12,6 +12,8 @@ on:
- '**/tutorial*.md'
- '**/slides.html'
- '**/slides/*.html'
- 'learning-pathways/*'
- 'faqs/**'

jobs:
lint:
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6 changes: 5 additions & 1 deletion _layouts/learning-pathway.html
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Expand Up @@ -46,8 +46,10 @@ <h2 id="requirements">Requirements</h2>
<h3 id="st-{{ section.section | slugify }}">{{ section.section }}</h3>
<p>{{ section.description | markdownify }}</p>

{% if section.tutorials %}
{% assign material_list = site | convert_to_material_list: section.tutorials %}
{% include _includes/tutorial_list.html sub=material_list %}
{% endif %}
{% endfor %}
</section>

Expand All @@ -56,12 +58,14 @@ <h3 id="st-{{ section.section | slugify }}">{{ section.section }}</h3>
<!-- Maintained by -->
<h2 id="editorial-board">Editorial Board</h2>
<p>This material is reviewed by our Editorial Board:</p>
{% assign editorial_board = pathway.maintainers %}
{% assign editorial_board = pathway.editorial_board %}
{% include _includes/contributor-list.html contributors=editorial_board badge=true %}

{% if pathway.funding %}
<h2 id="funders">Funders</h2>
<p>This material was funded by:</p>
{% assign funders = pathway.funding | sorted %}
{% include _includes/contributor-list.html contributors=funders badge=true %}
{% endif %}

</section>
Binary file added assets/images/wab-annotatedcells-2.png
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257 changes: 257 additions & 0 deletions json-ld.html
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---
layout: page
title: TeSS LD+JSON Tester
---

<p>
Here you can test how data from a page will be mapped to <a href="https://tess.elixir-europe.org/">TeSS</a> fields. This is based on <a href="https://docs.google.com/document/d/1qLbSgJmXA0xnuXaQl4gTvH0IR5K4sHNcGXsOQS5AMno/edit">this TeSS Document</a>
</p>

<div class="input-group">
<input class="form-control" id="input-url" type="text" value="topics/admin/tutorials/ansible-galaxy/tutorial.html">
<button id="submit" class="btn btn-primary">Submit</button>
</div>

<p>If you supply a full URL, your request will be proxied via <a href="https://corsproxy.io/">corsproxy.io</a></p>

<table class="table table-striped">
<thead>
<tr>
<th>Profile Property</th>
<th>marginality</th>
<th>Maps to TeSS</th>
<th>Notes/Vocab</th>
<th>🔍 Observed Value</th>
</tr>
</thead>
<tbody>
<tr id="t-name">
<td>name</td>
<td>minimum</td>
<td>Title</td>
<td>String</td>
<td></td>
</tr>
<tr id="t-description">
<td>description</td>
<td>minimum</td>
<td>Description</td>
<td>String: markdown-compatible</td>
<td></td>
</tr>
<tr id="t-url">
<td>url</td>
<td>recommended</td>
<td>URL</td>
<td></td>
<td></td>
</tr>
<tr id="t-keywords">
<td>keywords</td>
<td>minimum</td>
<td>Keywords</td>
<td>String: a comma separated list of keywords</td>
<td></td>
</tr>
<tr id="t-dateCreated">
<td>dateCreated</td>
<td>optional</td>
<td>Date</td>
<td></td>
<td></td>
</tr>
<tr id="t-license">
<td>license</td>
<td>recommended</td>
<td>License</td>
<td>Expects a SPDX identifier</td>
<td></td>
</tr>
<tr id="t-learningResourceType">
<td>learningResourceType</td>
<td>recommended</td>
<td>Resource Type</td>
<td>E.g. hands-on tutorials, etc</td>
<td></td>
</tr>
<tr id="t-about">
<td>about</td>
<td>recommended</td>
<td>Scientific Topics</td>
<td>Expects a DefinedTerm with a name property. EDAM</td>
<td></td>
</tr>
<tr id="t-audience">
<td>audience</td>
<td>recommended</td>
<td>Target Audience</td>
<td>Picks the audienceType property from the Audience</td>
<td></td>
</tr>
<tr id="t-author">
<td>author</td>
<td>recommended</td>
<td>Authors</td>
<td>Picks the name property from the Person</td>
<td></td>
</tr>
<tr id="t-contributor">
<td>contributor</td>
<td>optional</td>
<td>Contributors</td>
<td>Picks the name property from the Person</td>
<td></td>
</tr>
<tr id="t-identifier">
<td>identifier</td>
<td>recommended</td>
<td>DOI</td>
<td>Only recognizes DOI identifiers</td>
<td></td>
</tr>
<tr id="t-educationalLevel">
<td>educationalLevel</td>
<td>recommended</td>
<td>Difficulty Level</td>
<td>Beginner<br>Intermediate<br>Advanced</td>
<td></td>
</tr>
<tr id="t-abstract">
<td>abstract</td>
<td>recommended</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-competencyRequired">
<td>competencyRequired</td>
<td>recommended</td>
<td>Prerequisites</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-inLanguage">
<td>inLanguage</td>
<td>recommended</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-mentions">
<td>mentions</td>
<td>recommended</td>
<td></td>
<td>Seems to relate to External Resources</td>
<td></td>
</tr>
<tr id="t-teaches">
<td>teaches</td>
<td>recommended</td>
<td>Learning Objectives</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-timeRequired">
<td>timeRequired</td>
<td>recommended</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-accessibilitySummary">
<td>accessibilitySummary</td>
<td>optional</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-dateModified">
<td>dateModified</td>
<td>optional</td>
<td>Date modified</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-datePublished">
<td>datePublished</td>
<td>optional</td>
<td>Date published</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-creativeWorkStatus">
<td>creativeWorkStatus</td>
<td>optional</td>
<td>Status</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-version">
<td>version</td>
<td>optional</td>
<td>Version</td>
<td>Available in 1.4</td>
<td></td>
</tr>
<tr id="t-workTranslation">
<td>workTranslation</td>
<td>optional</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-recordedAt">
<td>recordedAt</td>
<td>optional</td>
<td></td>
<td>‘Link’ to Event via name, url pair of CourseInstance</td>
<td></td>
</tr>
<tr id="t-hasPart">
<td>hasPart</td>
<td>optional</td>
<td></td>
<td></td>
<td></td>
</tr>
<tr id="t-isPartOf">
<td>isPartOf</td>
<td>optional</td>
<td></td>
<td></td>
<td></td>
</tr>
</tbody>
</table>


<script>

document.getElementById("submit").onclick = function(){
var url = document.getElementById("input-url").value
if(url.slice(0, 8) === "https://") {
url = `https://corsproxy.io/?${url}`
}

fetch(url).then(function(response) {
// Once the page is loaded convert it to text
return response.text();
}).then(function(html) {
// Replace newlines to allow parsing more easily.
html = html.replaceAll(/[\n\r]/g, '');
// Parse the json-ld from the page
jsonld = JSON.parse(html.match(/<script type="application\/ld\+json">([^<]*)<\/script>/)[1]);

Object.keys(jsonld).forEach(k => {
e = document.getElementById(`t-${k}`)?.lastElementChild
if(e){e.innerText = JSON.stringify(jsonld[k])}
})
});
}
</script>

<style>
table tr :nth-child(5) {
font-family: monospace;
}
</style>
52 changes: 52 additions & 0 deletions learning-pathways/intro_single_cell.md
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---
layout: learning-pathway
tags: [beginner]
cover-image: assets/images/wab-annotatedcells-2.png
cover-image-alt: "Image of cells in different coloured clusters"
type: use

editorial_board:
- nomadscientist
- pavanvidem

title: Introduction to Galaxy and Single Cell RNA Sequence analysis
description: |
This learning path aims to teach you the basics of Galaxy and analysis of Single Cell RNA-seq data.
You will learn how to use Galaxy for analysis, and an important Galaxy feature for iterative single cell analysis. You'll tbe guided through the general theory of single analysis and then perform a basic analysis of 10X chromium data. For support throughout these tutorials, join our Galaxy [single cell chat group on Matrix](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im) to ask questions!
priority: 9

pathway:
- section: "Module 1: Introduction to Galaxy"
description: |
Get a first look at the Galaxy platform for data analysis. We start with a
short introduction (video slides & practical) to familiarize you with the Galaxy
interface, and then proceed with a short tutorial of how to tag - and organise! - your history.
tutorials:
- name: galaxy-intro-short
topic: introduction
- name: name-tags
topic: galaxy-interface

- section: "Module 2: Theory of Single-Cell RNA-seq"
description: |
When analysing sequencing data, you should always start with a quality control step to clean your data and make sure your data is good enough to answer your research question. After this step, you will often proceed with a mapping (alignment) or genome assembly step, depending on whether you have a reference genome to work with.
tutorials:
- name: scrna-intro
topic: single-cell

- section: "Module 3: Time to analyse data!"
description: |
It's time to apply your skills! You'll now analyse some clean data from the 10X Chromium platform.
tutorials:
- name: scrna-preprocessing-tenx
topic: single-cell
- name: scrna-scanpy-pbmc3k
topic: single-cell

- section: "The End!"
description: |
And now you're done! There are still loads of resources to take you from basic analysis to more difficult decision-making, deconvolution, multiomics, or ingesting from different data sources. See the [Galaxy Single Cell Training page](/training-material/topics/single-cell/index.html) for more!
---

New to Galaxy and/or the field of scRNA-seq? Follow this learning path to get familiar with the basics!

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