Skip to content

Commit

Permalink
squash 200+ commits
Browse files Browse the repository at this point in the history
  • Loading branch information
Retype GitHub Action authored and pdimens committed Dec 4, 2024
1 parent 004102c commit 2c378ef
Show file tree
Hide file tree
Showing 112 changed files with 26,052 additions and 3,294 deletions.
184 changes: 151 additions & 33 deletions 404.html

Large diffs are not rendered by default.

57 changes: 57 additions & 0 deletions blog/feed.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
<?xml version="1.0" encoding="UTF-8"?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>Blog</title>
<link>https://pdimens.github.io/harpy/blog/</link>
<description>Blog</description>
<copyright>© Copyright 2024. All rights reserved.</copyright>
<lastBuildDate>Tue, 05 Nov 2024 00:00:00 GMT</lastBuildDate>
<generator>https://retype.com</generator>
<atom:link rel="self" type="application/rss+xml" href="https://pdimens.github.io/harpy/blog/feed.xml" />
<image>
<title>Blog</title>
<link>https://pdimens.github.io/harpy/blog/</link>
<url>https://pdimens.github.io/harpy/favicon.png</url>
</image>
<item>
<title> Sort data by barcode</title>
<guid isPermaLink="true">https://pdimens.github.io/harpy/blog/sort_by_barcode/</guid>
<description>Sorting data by linked-read barcode</description>
<author>Pavel Dimens</author>
<pubDate>Tue, 05 Nov 2024 00:00:00 GMT</pubDate>
<category domain="https://pdimens.github.io/harpy/categories/guides/">guides</category>
</item>
<item>
<title> Simulating variants</title>
<guid isPermaLink="true">https://pdimens.github.io/harpy/blog/simulate_diploid/</guid>
<description>A realistic workflow to simulate variants</description>
<author>Pavel Dimens</author>
<pubDate>Mon, 30 Sep 2024 00:00:00 GMT</pubDate>
<category domain="https://pdimens.github.io/harpy/categories/guides/">guides</category>
</item>
<item>
<title> Pooling samples for SV calling</title>
<guid isPermaLink="true">https://pdimens.github.io/harpy/blog/sv_pooling/</guid>
<description>Why pool samples for SV calling and when to do it</description>
<author>Pavel Dimens</author>
<pubDate>Thu, 01 Aug 2024 00:00:00 GMT</pubDate>
<category domain="https://pdimens.github.io/harpy/categories/guides/">guides</category>
</item>
<item>
<title> Choosing a software runtime method</title>
<guid isPermaLink="true">https://pdimens.github.io/harpy/blog/software_environments/</guid>
<description>Deciding between using Conda or Containers</description>
<author>Pavel Dimens</author>
<pubDate>Fri, 21 Jun 2024 00:00:00 GMT</pubDate>
<category domain="https://pdimens.github.io/harpy/categories/guides/">guides</category>
</item>
<item>
<title> Filtering Variants</title>
<guid isPermaLink="true">https://pdimens.github.io/harpy/blog/filtering_snps/</guid>
<description>A gentle introduction to the wild world of filtering SNPs</description>
<author>Pavel Dimens</author>
<pubDate>Wed, 05 Jun 2024 00:00:00 GMT</pubDate>
<category domain="https://pdimens.github.io/harpy/categories/guides/">guides</category>
</item>
</channel>
</rss>
467 changes: 467 additions & 0 deletions blog/filtering_snps/index.html

Large diffs are not rendered by default.

400 changes: 400 additions & 0 deletions blog/index.html

Large diffs are not rendered by default.

640 changes: 640 additions & 0 deletions blog/simulate_diploid/index.html

Large diffs are not rendered by default.

528 changes: 528 additions & 0 deletions blog/software_environments/index.html

Large diffs are not rendered by default.

485 changes: 485 additions & 0 deletions blog/sort_by_barcode/index.html

Large diffs are not rendered by default.

561 changes: 561 additions & 0 deletions blog/sv_pooling/index.html

Large diffs are not rendered by default.

402 changes: 402 additions & 0 deletions categories/guides/index.html

Large diffs are not rendered by default.

342 changes: 342 additions & 0 deletions categories/index.html

Large diffs are not rendered by default.

637 changes: 637 additions & 0 deletions commonoptions/index.html

Large diffs are not rendered by default.

622 changes: 622 additions & 0 deletions development/index.html

Large diffs are not rendered by default.

Binary file removed favicon.png
Binary file not shown.
610 changes: 610 additions & 0 deletions haplotagdata/index.html

Large diffs are not rendered by default.

378 changes: 295 additions & 83 deletions index.html

Large diffs are not rendered by default.

297 changes: 241 additions & 56 deletions install/index.html

Large diffs are not rendered by default.

599 changes: 0 additions & 599 deletions modules/imputation/index.html

This file was deleted.

382 changes: 0 additions & 382 deletions modules/initialization/index.html

This file was deleted.

377 changes: 0 additions & 377 deletions modules/phasing/index.html

This file was deleted.

355 changes: 0 additions & 355 deletions modules/qualitytrimming/index.html

This file was deleted.

444 changes: 0 additions & 444 deletions modules/readmapping/index.html

This file was deleted.

418 changes: 0 additions & 418 deletions modules/variantcalling/index.html

This file was deleted.

4 changes: 2 additions & 2 deletions resources/css/katex.css

Large diffs are not rendered by default.

6 changes: 3 additions & 3 deletions resources/css/retype.css

Large diffs are not rendered by default.

Binary file added resources/fonts/Inter-italic-latin-var.woff2
Binary file not shown.
Binary file added resources/fonts/Inter-roman-latin-var.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-Medium-Latin.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-Medium-LatinExt.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-Regular-Latin.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-Regular-LatinExt.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-SemiBold-Latin.woff2
Binary file not shown.
Binary file removed resources/fonts/Poppins-SemiBold-LatinExt.woff2
Binary file not shown.
2 changes: 1 addition & 1 deletion resources/js/config.js

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions resources/js/katex.js

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions resources/js/lunr.js

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions resources/js/mermaid.js

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions resources/js/prism.js

Large diffs are not rendered by default.

14 changes: 7 additions & 7 deletions resources/js/retype.js

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion resources/js/search.json

Large diffs are not rendered by default.

20 changes: 19 additions & 1 deletion resources/mermaid.js.LICENSE.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,22 @@
/*! For license information please see mermaid.esm.min.mjs.LICENSE.txt */
/*!
* Wait for document loaded before starting the execution
*/

/*!
Embeddable Minimum Strictly-Compliant Promises/A+ 1.1.1 Thenable
Copyright (c) 2013-2014 Ralf S. Engelschall (http://engelschall.com)
Licensed under The MIT License (http://opensource.org/licenses/MIT)
*/

/*! @license DOMPurify 3.0.5 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.0.5/LICENSE */

/*! Bezier curve function generator. Copyright Gaetan Renaudeau. MIT License: http://en.wikipedia.org/wiki/MIT_License */

/*! Check if previously processed */

/*! Runge-Kutta spring physics function generator. Adapted from Framer.js, copyright Koen Bok. MIT License: http://en.wikipedia.org/wiki/MIT_License */

/*! js-yaml 4.1.0 https://github.com/nodeca/js-yaml @license MIT */

/**
* Mermaid is a Javascript based diagramming and charting tool that uses Markdown-inspired text definitions and a renderer to create and modify complex diagrams.
Expand Down
2 changes: 1 addition & 1 deletion resources/retype.LICENSE.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Retype Software License Agreement

Version 2.4.0
Version 3.6.0

THIS DOCUMENT IS A LEGAL AGREEMENT (the "License Agreement") BETWEEN OBJECT.NET, INC. ("We," "Us")
AND YOU OR THE ORGANIZATION ON WHOSE BEHALF YOU ARE UNDERTAKING THE LICENSE DESCRIBED BELOW ("You",
Expand Down
4 changes: 3 additions & 1 deletion resources/retype.js.LICENSE.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
/*!
* clipboard.js v2.0.10
* clipboard.js v2.0.11
* https://clipboardjs.com/
*
* Licensed MIT © Zeno Rocha
*/

/*! MIT License. Copyright 2015-2018 Richard Moore <me@ricmoo.com>. See LICENSE.txt. */
2 changes: 1 addition & 1 deletion robots.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
User-agent: *
Allow: /

Sitemap: /sitemap.xml.gz
Sitemap: https://pdimens.github.io/harpy/sitemap.xml.gz
Binary file modified sitemap.xml.gz
Binary file not shown.
462 changes: 462 additions & 0 deletions snakemake/index.html

Large diffs are not rendered by default.

386 changes: 315 additions & 71 deletions software/index.html

Large diffs are not rendered by default.

Binary file added static/assembly_multiqc.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added static/assembly_quast.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added static/bc_threshold.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit 2c378ef

Please sign in to comment.