Merge branch 'master' into hackathon23

nf-core · Jul 6, 2023 · bc8e07f · bc8e07f
2 parents 2a5f670 + d755251
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diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -28,7 +28,11 @@ Please note that the list above is alphabetised and is therefore not ranked in a
 
 An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about).
 
-Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer.
+Our Safety Officers are
+
+- [@ctuni](https://github.com/ctuni): Cris Tuñí ([contact](mailto:[email protected]))
+- [@heuermh](https://github.com/heuermh): Michael Heuer ([contact](mailto:[email protected]))
+- [@snafees](https://github.com/snafees/): Saba Nafees ([contact](mailto:[email protected]))
 
 nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
 

diff --git a/composer.json b/composer.json
@@ -7,6 +7,6 @@
         "erusev/parsedown": "1.8.0-beta-7",
         "erusev/parsedown-extra": "0.8.0-beta-1",
         "mustangostang/spyc": "=0.6.2",
-        "symfony/yaml": "^5.3"
+        "symfony/yaml": "5.3"
     }
 }
diff --git a/composer.lock b/composer.lock
diff --git a/includes/footer.php b/includes/footer.php
@@ -30,6 +30,9 @@
             <a href="/about#czi-eoss">
               <img src="/assets/img/contributors-colour/CZI-alt.svg" alt="CZI" class="" style="max-width: 50px">
             </a>,
+            <a href="/about#seqera">
+              <img src="/assets/img/seqera-icon.svg" alt="Seqera" class="" style="max-width: 50px">
+            </a>,
             <a href="/about#microsoft-azure">
               <img src="/assets/img/contributors-colour/azure.svg" alt="Microsoft Azure" style="max-width: 50px">
             </a>

diff --git a/includes/functions.php b/includes/functions.php
@@ -447,19 +447,28 @@ function ($matches) use ($heading_ids, $is_hidden) {
             $hid = preg_replace('/^[\s\-]+/', '', $hid); // remove dashes from start of string (e.g. for parameter)
             $heading_ids[] = $hid;
             $hidden_class = $is_hidden ? 'toc-hidden' : '';
-            return '<h' .
-                $matches[1] .
-                ' id="' .
-                $hid .
-                '" class="' .
-                $hidden_class .
-                '">' .
-                $matches[2] .
-                '<a href="#' .
-                $hid .
-                '" class="header-link scroll_to_link"><span class="fas fa-link fa-xs ms-1"></span></a></h' .
-                $matches[3] .
-                '>';
+            $to_return = '<h' . $matches[1] . ' id="' . $hid . '" class="' . $hidden_class . '">';
+            if (strpos($matches[2], '<code>')) {
+                $to_return .=
+                    $to_return .
+                    '<a href="#' .
+                    $hid .
+                    '" class="header-link parameter-link scroll_to_link"><span class="fas fa-link fa-xs me-2"></span></a>' .
+                    $matches[2] .
+                    '</h' .
+                    $matches[3] .
+                    '>';
+            } else {
+                $to_return .=
+                    $to_return .
+                    $matches[2] .
+                    ' <a href="#' .
+                    $hid .
+                    '" class="header-link scroll_to_link"><span class="fas fa-link fa-xs ms-1"></span></a></h' .
+                    $matches[3] .
+                    '>';
+            }
+            return $to_return;
         },
         $content_input,
     );

diff --git a/includes/header.php b/includes/header.php
@@ -194,8 +194,8 @@ function gtag() {
         <div class="container">
           <?php
           if (isset($md_github_url) and $md_github_url) {
-              $md_github_url = str_replace('/contributing/', '/developers/', $md_github_url);
-              $md_github_url = str_replace('/docs', '', $md_github_url);
+              $md_github_url = str_replace('/docs/contributing/', '/developers/', $md_github_url);
+              $md_github_url = str_replace('/docs/usage/', '/usage/', $md_github_url);
               echo '<a href="' .
                   $md_github_url .
                   '" class="edit-md-btn btn btn-sm btn-outline-light float-end d-none d-md-inline-block ms-2 mt-4 d-print-none" title="Edit this page on GitHub" data-bs-toggle="tooltip" data-bs-delay=\'{ "show": 500, "hide": 0 }\'><i class="fas fa-pencil-alt"></i> Edit</a>';

diff --git a/includes/parse_md.php b/includes/parse_md.php
@@ -154,8 +154,8 @@ function ($match) {
             '<div class="row flex-wrap-reverse flex-lg-wrap"><div class="col-12 col-lg-9">
                       <div class="rendered-markdown publication-page-content">' .
             $content .
-            # '</div>'. # Removing fixes the ToC for the hackathon event page. Not sure why. TODO: May break other stuff
-            '</div>';
+            '</div>
+                </div>';
         # sidebar
         $content .= '<div class="col-12 col-lg-3 ps-2 h-100 sticky-top"><div class="side-sub-subnav">';
         # ToC

diff --git a/includes/pipeline_page/docs_md.php b/includes/pipeline_page/docs_md.php
@@ -44,9 +44,6 @@
 $src_url_prepend = 'https://raw.githubusercontent.com/nf-core' . $href_url_prepend;
 $href_url_suffix_cleanup = '\.md';
 
-# Footer link
-$md_github_url = 'https://github.com/' . $pipeline->full_name . '/blob/' . $release . '/' . $filename;
-
 # Markdown cleanup
 $md_content_replace[] = ['/# nf-core\/' . $pipeline->name . ': /', '# '];
 $md_content_replace[] = [

diff --git a/markdown/about.md b/markdown/about.md
@@ -52,7 +52,6 @@ The current members of the maintainer's team in 2023 are: <!-- TODO: check if ye
 - [@Emiller88](https://github.com/Emiller88): Edmund Miller (University of Texas at Dallas & Element Biosciences)
 - [@FriederikeHanssen](https://github.com/FriederikeHanssen): Friederike Hanssen (Quantitative Biology Center, QBiC, University of Tübingen)
 - [@mirpedrol](https://github.com/mirpedrol): Júlia Mir Pedrol (Quantitative Biology Center, QBiC, University of Tübingen)
-- [@ggabernet](https://github.com/ggabernet): Gisela Gabernet (Quantitative Biology Center, QBiC, University of Tübingen)
 - [@drpatelh](https://github.com/drpatelh): Harshil Patel (Seqera Labs)
 - [@jfy133](https://github.com/jfy133): James A. Fellows Yates (Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute & Max Planck Institute - for Evolutionary Anthropology)
 - [@jasmezz](https://github.com/jasmezz): Jasmin Frangenberg (Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute)
@@ -86,9 +85,9 @@ The safety team is responsible for ensuring the community is a safe place and re
 
 The current safety team in 2023 are:
 
-- [@ctuni](https://t.co/mQInuSXc5R) Cris Tuñí
-- [@heuerm](https://github.com/heuermh) Michael Heuer
-- [@snafees](https://github.com/snafees/) Saba Nafees
+- [@ctuni](https://github.com/ctuni): Cris Tuñí ([contact](mailto:[email protected]))
+- [@heuermh](https://github.com/heuermh): Michael Heuer ([contact](mailto:[email protected]))
+- [@snafees](https://github.com/snafees/): Saba Nafees ([contact](mailto:[email protected]))
 
 ## Financial Support
 
@@ -125,6 +124,24 @@ The CZI grant employs personnel based at the [SciLifeLab National Genomics Infra
 
 <div class="clearfix"></div>
 
+### Seqera Labs {#seqera}
+
+<img src="/assets/img/contributors-colour/seqera.svg" alt="Seqera Labs" class="float-end darkmode-image me-5 mb-5 w-25 ms-3">
+
+Seqera Labs is the leading provider of open source workflow orchestration software needed for data pipeline processing, cloud infrastructure, and secure collaboration.
+
+Seqera is the company behind Nextflow and has supported the nf-core community since its inception.
+
+Specifically, Seqera helps nf-core with:
+
+- Event organisation and costs
+- Website hosting
+- Employment of several core contributors
+- A [Tower Cloud Professional](https://cloud.tower.nf/pricing/) account for launching and managing full-size release tests.
+- Providing and maintaining Nextflow! ✨
+
+<div class="clearfix"></div>
+
 ### SciLifeLab Data Centre
 
 <img src="/assets/img/contributors-colour/SciLifeLabDC.svg" alt="SciLifeLab Data Centre" class="float-end darkmode-image me-5 mb-5 w-25 ms-3">
@@ -155,6 +172,28 @@ You will soon be able to explore and download these pipeline results on the nf-c
 
 <div class="clearfix"></div>
 
+## Open Source Support
+
+We also thank the following organisations for supporting nf-core through providing us 'open source plans' of their services:
+
+<div class="row my-5">
+  <div class="col-lg-4" style="align-self:center;">
+    <a href="https://www.docker.com/" target="_blank">
+      <img src="/assets/img/docker-horizontal.png" alt="Docker w-100">
+    </a>
+  </div>
+  <div class="col-lg-4" style="align-self:center;">
+    <a href="https://gitpod.io/" target="_blank">
+      <img src="/assets/img/contributors-colour/gitpod.svg" alt="Gitpod" class="darkmode-image w-100">
+    </a>
+  </div>
+  <div class="col-lg-4" style="align-self:center;">
+    <a href="https://hackmd.io/" target="_blank">
+      <img src="/assets/img/contributors-colour/hackmd.svg" alt="HackMD" class="darkmode-image w-100">
+    </a>
+  </div>
+</div>
+
 ## History of nf-core
 
 The nf-core project came about at the start of 2018. [Phil Ewels](http://phil.ewels.co.uk/) ([@ewels](https://github.com/ewels/)) was the head of the development facility at [NGI Stockholm](https://ngisweden.scilifelab.se/) (National Genomics Infrastructure), part of [SciLifeLab](https://www.scilifelab.se/) in Sweden.