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Major tidy up of the repository and the website #61

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merged 80 commits into from
Mar 7, 2024
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f33fe94
Folded the team description into the main sanger-tol document
muffato Feb 29, 2024
3c68db0
Should be lower case
muffato Feb 29, 2024
7b4fb73
Removed the bytesizes since they are nf-core events, not sanger-tol
muffato Feb 29, 2024
9074e27
Added more events
muffato Feb 29, 2024
8979bdc
Not needed
muffato Feb 29, 2024
429b96a
We should be able to call assets directly
muffato Feb 29, 2024
dc06dfb
This should remove the margins
muffato Feb 29, 2024
5e17daa
I can be the point of contact
muffato Feb 29, 2024
e498c2c
Added ENA
muffato Feb 29, 2024
8e7e74c
We are sanger-tol, not nf-core
muffato Feb 29, 2024
877bebc
Wrong heading
muffato Feb 29, 2024
01eb3a4
More updates
muffato Feb 29, 2024
48074a3
I can be the point of contact
muffato Feb 29, 2024
925a831
typo
muffato Feb 29, 2024
5cc7b67
Missing heading
muffato Feb 29, 2024
3b087e4
More videos !
muffato Feb 29, 2024
edf35c5
Added BGA
muffato Feb 29, 2024
1609b6b
Use relative links
muffato Feb 29, 2024
933ea33
Fixed the link
muffato Feb 29, 2024
685343d
[prettier]
muffato Feb 29, 2024
3b1b70d
Removed some occurrences of nf-core and the rich-codex integration
muffato Feb 29, 2024
c1f72e9
Cleaned up some images
muffato Feb 29, 2024
cd303f5
Not used anywhere
muffato Feb 29, 2024
ef635d3
Not used anywhere
muffato Feb 29, 2024
710770b
Not used
muffato Feb 29, 2024
2934891
We don't need the .ai files
muffato Feb 29, 2024
86edd72
Removed an absolute link
muffato Feb 29, 2024
7beb3f7
Updated title
muffato Feb 29, 2024
6ec2dc6
Imported all the documentation from the wikis (incl. Confluence)
muffato Feb 29, 2024
be32f59
[prettier]
muffato Feb 29, 2024
adcaafc
Removed the size constraint
muffato Feb 29, 2024
de37d06
Added some text about using Nextflow on the farm
muffato Feb 29, 2024
2a6e6ec
Typos (most found by codespell)
muffato Feb 29, 2024
483a31b
We don't need the .ai files
muffato Feb 29, 2024
fde9585
Consolidated projects and tools under the same Resources menu
muffato Feb 29, 2024
a145394
typo
muffato Feb 29, 2024
b3da265
Further tidy up
muffato Feb 29, 2024
a2b7a86
Added a placeholder docs/usage page
muffato Feb 29, 2024
d32c1b9
Right location
muffato Feb 29, 2024
8867e26
[prettier]
muffato Feb 29, 2024
361c4c1
The nf-core intro fits better at the end
muffato Feb 29, 2024
791b1c0
typo
muffato Mar 1, 2024
4091531
URLs should be protected with anchors
muffato Mar 2, 2024
da49a9d
Restored the config file as it may become useful in the future
muffato Mar 6, 2024
13e47c2
Less confusing description of the main branch
muffato Mar 6, 2024
3d44d9f
Easier to read with some whitespace
muffato Mar 6, 2024
2482ea6
Update markdown/developers/env.md
muffato Mar 6, 2024
f8b6884
`tw launch` needs access to the actual repository, not the documentation
muffato Mar 6, 2024
afe893f
Unncessary heading
muffato Mar 6, 2024
eb76635
Added links to the websites
muffato Mar 6, 2024
082f556
There were too many "About" !
muffato Mar 6, 2024
13d52a9
s/Tower/Seqera Platform/g
muffato Mar 6, 2024
b485f5a
Clarified the part about using the oversubscribed queue
muffato Mar 6, 2024
8849327
Fixed the yaml files of the events
muffato Mar 6, 2024
746d764
Wrong syntax here too
muffato Mar 6, 2024
f4bb672
Wrong syntax here too
muffato Mar 6, 2024
29a5e71
"connect to" sounds better
muffato Mar 6, 2024
c4648b1
"tutorial" is a more appropriate type
muffato Mar 6, 2024
da3e0e7
Synchronised the entry with the nf-co.re one
muffato Mar 6, 2024
c020d0c
Added the symposium
muffato Mar 6, 2024
55e757d
Added missing nf-core hackathons
muffato Mar 7, 2024
f43f965
More training
muffato Mar 7, 2024
5d9c9df
We don't do these kinds of events yet. Commenting for now
muffato Mar 7, 2024
452531e
Added anotehr training event
muffato Mar 7, 2024
3d4e666
Fixed the layout
muffato Mar 7, 2024
26e418c
Last link
muffato Mar 7, 2024
189e6d6
[prettier]
muffato Mar 7, 2024
cb164e6
Adding credits
muffato Mar 7, 2024
93467dc
Adding credits
muffato Mar 7, 2024
4d66b2d
Trying to fix the link
muffato Mar 7, 2024
e52f85c
Trying to fix the link
muffato Mar 7, 2024
bae44cf
Added the two Nextflow Summits
muffato Mar 7, 2024
aadcb91
Removed broken and unneeded links
muffato Mar 7, 2024
d8a7300
Adding credits
muffato Mar 7, 2024
117f79b
Added a heading
muffato Mar 7, 2024
9567467
We need at least two headings
muffato Mar 7, 2024
ce76675
Added video recordings
muffato Mar 7, 2024
e070b0c
Added another Nextflow in Action
muffato Mar 7, 2024
4386cfb
Wrong link
muffato Mar 7, 2024
b2727c0
[prettier]
muffato Mar 7, 2024
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4 changes: 2 additions & 2 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Hi there! Many thanks for taking an interest in improving the sanger-tol website
If you'd like to write some code for sanger-tol/pipelines-website, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the
[sanger-tol/pipelines-website issues](<[https://github.com/nf-core/nf-co.re/issues](https://github.com/sanger-tol/pipelines-website/issues)>) to avoid duplicating work.
[sanger-tol/pipelines-website issues](https://github.com/sanger-tol/pipelines-website/issues) to avoid duplicating work.
- If there isn't one already, please create one so that others know you're working on this
2. Fork the [sanger-tol/pipelines-website repository](https://github.com/sanger-tol/pipelines-website) to your GitHub account
3. Make the necessary changes / additions within your forked repository
Expand All @@ -23,4 +23,4 @@ For now, the only test is for Markdown syntax, using the `markdownlint` package.

## Getting help

For further information or help, please [contact us](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=priyanka-surana%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
For further information or help, please [contact us](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/add_team.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ description: Add details to include your team details to the website
title: '[Team]: '
labels: ['team', 'enhancement']
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
attributes:
Expand Down
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/add_team_members.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ description: Add your details to the team page on the website
title: '[Team member]: '
labels: ['team', 'enhancement']
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
attributes:
Expand Down
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/add_team_projects.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ description: Add project details to include in team page on the website
title: '[Project]: '
labels: ['team', 'enhancement']
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
attributes:
Expand Down
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/add_tool.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ description: Add details to include your tool to the website
title: '[Tool]: '
labels: ['tool', 'enhancement']
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
attributes:
Expand Down
1 change: 0 additions & 1 deletion .github/ISSUE_TEMPLATE/contact_us.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ description: Get in touch with the Tree of Life informatics teams.
title: '[Contact Us]: '
labels: ['connect']
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
Expand Down
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/publications.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: Add publications
description: Add publication to the sanger-tol website
title: '[Publication]: DOI'
assignees:
- priyanka-surana
- muffato
body:
- type: markdown
attributes:
Expand Down
48 changes: 0 additions & 48 deletions .github/rich-codex.yml

This file was deleted.

31 changes: 0 additions & 31 deletions .github/workflows/rich-codex.yml

This file was deleted.

3 changes: 1 addition & 2 deletions .prettierignore
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ public_html/tools/docs/
nfcore_stats.json
nfcore_issue_stats.json
markdown/pipelines
markdown/tools
api_cache
contributor_stats
update.log
Expand All @@ -43,4 +42,4 @@ php.ini
node_modules
vendor
backstop_data
.mysql-data/
.mysql-data/
4 changes: 2 additions & 2 deletions CODE_OF_CONDUCT.md
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ Members of the Safety Team (the Safety Officers) are responsible for clarifying

The Safety Team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.

Members of the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.
Members of the Safety Team who violate the CoC will be required to recurse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.

## When and where does this Code of Conduct apply?

Expand Down Expand Up @@ -122,7 +122,7 @@ After you file a report, one or more members of our Safety Team will contact you

All reports will be read and handled by the members of the Safety Team at sanger-tol.

If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups.
If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recurse themselves as per our Code of Conduct and will not have access to any follow-ups.

To keep this first report confidential from any of the Safety Team members, please submit your first report by direct email to any of the safety officers you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with.

Expand Down
7 changes: 4 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ docker compose up
You should then be able to access the website in your browser at [http://localhost:8888/](http://localhost:8888/).

If you prefer, you can also use a tool such as [MAMP](https://www.mamp.info/) - if so,
set the base directory to `/path/to/nf-co.re/public_html` in _Preferences > Web-Server > Document Root_ and then hit _Start Servers_.
set the base directory to `/path/to/pipelines-website/public_html` in _Preferences > Web-Server > Document Root_ and then hit _Start Servers_.

Most of the hand-written text is in `/markdown`, to make it easier to write. The PHP files in `/public_html` then parse this into HTML dynamically, if supplied with a filename.

Expand Down Expand Up @@ -160,11 +160,12 @@ If you are looking forward to contribute to the website or add your institution

## Community

If you have any questions or issues, please [let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=priyanka-surana%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).
If you have any questions or issues, please [let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato%2Cmuffato&labels=connect&projects=&template=contact_us.yaml&title=%5BContact+Us%5D%3A+).

## Credits

Priyanka Surana ([@priyanka-surana](http://github.com/priyanka-surana/)) manages the content and Guoying Qi ([@gq1](https://github.com/gq1)) manages the website. Many individuals, especially Matthieu Muffato ([@muffato](http://github.com/muffato)), have made various contributions.
Matthieu Muffato ([@muffato](http://github.com/muffato)) manages the content and Guoying Qi ([@gq1](https://github.com/gq1)) manages the website.
Many individuals, especially Priyanka Surana ([@priyanka-surana](http://github.com/priyanka-surana/)), have made various contributions.

Phil Ewels ([@ewels](http://github.com/ewels/)) built the original nf-core website.
More recently, [@mashehu](https://github.com/mashehu) has done a great deal of work with the code.
Expand Down
4 changes: 2 additions & 2 deletions composer.json
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "nf-core/nf-co.re",
"description": "PHP dependencies for the main nf-core website.",
"name": "sanger-tol/pipelines-website",
"description": "PHP dependencies for the sanger-tol pipelines website.",
"require": {
"abraham/twitteroauth": "^2.0",
"spatie/calendar-links": "1.8",
Expand Down
36 changes: 14 additions & 22 deletions includes/footer.php
Original file line number Diff line number Diff line change
Expand Up @@ -86,43 +86,35 @@

</div>
<div class="col-sm-6 col-lg-3 offset-lg-1 mb-3 d-print-none">
<h5>Getting Started</h5>
<h5>Our documentation</h5>
<ul class="list-unstyled">
<li><a href="/pipelines">Available pipelines</a></li>
<li><a href="/modules">nf-core modules</a></li>
<li><a href="https://nf-co.re/tools">nf-core tools</a></li>
<li><a href="https://nf-co.re/docs/usage/introduction">Getting started</a></li>
<li><a href="https://nf-co.re/docs/usage/installation">Installation</a></li>
<li><a href="https://nf-co.re/docs/usage/configuration">Pipeline configuration</a></li>
<li><a href="https://nf-co.re/docs/usage/offline">Running offline</a></li>
<li><a href="https://nf-co.re/docs/usage/tutorials">Usage tutorials</a></li>
<li><a href="https://nf-co.re/docs/usage/data_management">Data Management</a></li>
<li><a href="https://nf-co.re/docs/usage/troubleshooting">Troubleshooting</a></li>
<li><a href="https://nf-co.re/docs/usage/tutorials/nextflow">Nextflow resources</a></li>
<li><a href="/pipelines">Pipelines</a></li>
<li><a href="/tools">Tools</a></li>
<li><a href="/docs/contributing/modules">Modules</a></li>
<li><a href="/docs/contributing/review_checklist">Code review</a></li>
</ul>
</div>
<div class="col-sm-6 col-lg-3 mb-3 d-print-none">
<h5>For Authors</h5>
<h5>nf-core documentation</h5>
<ul class="list-unstyled">
<li><a href="https://nf-co.re/docs/contributing/modules">DSL2 modules</a></li>
<li><a href="https://nf-co.re/docs/contributing/subworkflows">DSL2 subworkflows</a></li>
<li><a href="https://nf-co.re/docs/contributing/training_guide">Training guide</a></li>
<li><a href="https://nf-co.re/docs/contributing/sync">Template synchronisation</a></li>
<li><a href="https://nf-co.re/docs/contributing/tutorials">Developer tutorials</a></li>
<li><a href="https://nf-co.re/docs/contributing/editor_plugins">Code editor plugins</a></li>
<li><a href="https://nf-co.re/docs/contributing/design_guidelines">Graphic design guidelines</a></li>
<li><a href="https://nf-co.re/docs/usage/introduction">Getting started</a></li>
<li><a href="https://nf-co.re/docs/usage/installation">Installation</a></li>
<li><a href="https://nf-co.re/docs/usage/tutorials">Usage tutorials</a></li>
<li><a href="https://nf-co.re/docs/usage/tutorials/nextflow">Nextflow resources</a></li>
<li><a href="https://nf-co.re/tools">Command-line tool</a></li>
<li><a href="https://nf-co.re/modules">Modules</a></li>
</ul>
</div>
<div class="col-sm-6 col-lg-2 mb-3 d-print-none">
<h5>About sanger-tol</h5>
<h5>More information</h5>
<ul class="list-unstyled">
<li><a href="/about">About sanger-tol</a></li>
<li><a href="/events">Events</a></li>
<li><a href="/community">Community</a></li>
<li><a href="/stats">Statistics</a></li>
<li><a href="/publications">Publications</a></li>
<li><a href="/code_of_conduct">Code of conduct</a></li>
<li><a href="/join" class="mt-1 btn btn-outline-success">Join sanger-tol</a></li>
<li><a href="/connect" class="mt-1 btn btn-outline-success">Connect with sanger-tol</a></li>
</ul>
</div>
</div>
Expand Down
38 changes: 14 additions & 24 deletions includes/header.php
Original file line number Diff line number Diff line change
Expand Up @@ -135,34 +135,24 @@ function gtag() {
</button>
<div class="collapse navbar-collapse justify-content-md-center" id="navbarCollapse">
<ul class="navbar-nav">

<li class="nav-item p-1">
<a class="nav-link" href="/">Home</a>
</li>

<li class="nav-item p-1">
<a class="nav-link" href="/pipelines">Pipelines</a>
</li>

<li class="nav-item p-1 dropdown">
<a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Teams</a>
<div class="dropdown-menu">
<a class="dropdown-item" href="/it">Informatics Infrastructure (IT)</a>
</div>
</li>

<li class="nav-item p-1 dropdown">
<a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Projects</a>
<a class="nav-link dropdown-toggle" href="/about" role="button" data-bs-toggle="dropdown">Resources</a>
<div class="dropdown-menu">
<a class="dropdown-item" href="/genome_after_party">Genome After Party</a>
<a class="dropdown-item" href="/tools">Tools</a>
</div>
</li>

<li class="nav-item p-1">
<a class="nav-link" href="/pipelines">Pipelines</a>
</li>

<li class="nav-item p-1">
<a class="nav-link" href="/tools/">Tools</a>
</li>

<li class="nav-item p-1">
<li class="nav-item p-1">
<a class="nav-link" href="/docs">Docs</a>
</li>

Expand All @@ -183,18 +173,18 @@ function gtag() {
<a class="dropdown-item" href="/stats">Statistics</a>
<a class="dropdown-item" href="/publications">Publications</a>
<a class="dropdown-item" href="/code_of_conduct">Code of conduct</a>
<a class="dropdown-item" href="/join">Join sanger-tol</a>
<a class="dropdown-item" href="/connect">Connect with sanger-tol</a>
</div>
</li>

</ul>

<hr class="d-md-none">
<a class="d-md-none btn d-block btn-success mb-3" href="/join">
Join sanger-tol
<a class="d-md-none btn d-block btn-success mb-3" href="/connect">
Connect with sanger-tol
</a>
<a class="d-none d-lg-block btn btn-success" style="position:absolute; right: 1rem;" href="/join">
Join sanger-tol
<a class="d-none d-lg-block btn btn-success" style="position:absolute; right: 1rem;" href="/connect">
Connect with sanger-tol
</a>

</div>
Expand All @@ -208,7 +198,7 @@ function gtag() {
<div class="container">
<?php
if (isset($md_github_url) and $md_github_url) {
$md_github_url = str_replace('/docs/contributing/', '/developers/', $md_github_url);
$md_github_url = str_replace('/docs/contributing/', '/contributing/', $md_github_url);
$md_github_url = str_replace('/docs/usage/', '/usage/', $md_github_url);
echo '<a href="' .
$md_github_url .
Expand Down
2 changes: 1 addition & 1 deletion includes/module_page/_index.php
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
}
}
mysqli_close($conn);
// function to create bootstrap row with the first column for the name and type and the second for the descritption
// function to create bootstrap row with the first column for the name and type and the second for the description
function create_row($name, $type, $description, $pattern) {
$id = strtolower(preg_replace('/[^\w\-\.]+/', '', str_replace(' ', '-', $name)));
$id = str_replace('.', '-', $id); // periods break the js code, because they are not valid in selector ids
Expand Down
6 changes: 3 additions & 3 deletions includes/pipeline_page/sidebar.php
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@
<button class="nav-link text-muted" id="nf-tab" data-bs-toggle="tab" data-bs-target="#nf" type="button" role="tab" aria-controls="nf" aria-selected="false">Nextflow</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link text-muted" id="tw-tab" data-bs-toggle="tab" data-bs-target="#tw" type="button" role="tab" aria-controls="tw" aria-selected="false">Tower</button>
<button class="nav-link text-muted" id="tw-tab" data-bs-toggle="tab" data-bs-target="#tw" type="button" role="tab" aria-controls="tw" aria-selected="false">Seqera Platform</button>
</li>
</ul>
<div class="tab-content mt-2">
Expand All @@ -91,10 +91,10 @@
</div>
<div class="tab-pane" id="tw" role="tabpanel" aria-labelledby="tw-tab">
<div class=" input-group input-group-sm pipeline-run-cmd">
<input type="text" class="form-control input-sm code rounded-0" id="pipeline-tw-run-cmd-text" data-autoselect="" value="tw launch https://nf-co.re/<?php echo $pipeline->name .
<input type="text" class="form-control input-sm code rounded-0" id="pipeline-tw-run-cmd-text" data-autoselect="" value="tw launch https://github.com/sanger-tol/<?php echo $pipeline->name .
$release_cmd; ?>" aria-label="Copy run command" readonly="">
<button class="btn btn-outline-secondary copy-txt rounded-0" data-bs-target="pipeline-tw-run-cmd-text" data-bs-toggle="tooltip" data-bs-placement="left" title="Copy to clipboard" type="button"><i class="fas fa-clipboard px-1"></i></button>
</div><p class="text-muted">Read how to configure the Tower CLI <u><a href='https://github.com/seqeralabs/tower-cli/#2-configuration' target="_blank">here</a></u>.</p></div>
</div><p class="text-muted">Read how to configure the Seqera Platform CLI <u><a href='https://github.com/seqeralabs/tower-cli/#2-configuration' target="_blank">here</a></u>.</p></div>
</div>
</div>
</div>
Expand Down
2 changes: 1 addition & 1 deletion includes/search_results.php
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
require '../vendor/autoload.php';
use Spyc;

// $search_term - should be availble from include
// $search_term - should be available from include
$search_results = [
'pipelines' => [],
'documentation' => [],
Expand Down
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