-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Deployed 83ea1cc to v5.2.0 with MkDocs 1.5.3 and mike 2.0.0
- Loading branch information
1 parent
198701a
commit 3febb12
Showing
45 changed files
with
5,899 additions
and
6 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| v5.1.0 | ||
| v5.2.0 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| v5.1.0 | ||
| v5.2.0 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,146 @@ | ||
| <!DOCTYPE html> | ||
| <html class="writer-html5" lang="en" > | ||
| <head> | ||
| <meta charset="utf-8" /> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge" /> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0" /> | ||
| <link rel="shortcut icon" href="/img/favicon.ico" /> | ||
| <title>pipeline-call-gSV</title> | ||
| <link rel="stylesheet" href="/css/theme.css" /> | ||
| <link rel="stylesheet" href="/css/theme_extra.css" /> | ||
| <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" /> | ||
| <link href="/css/version-select.css" rel="stylesheet" /> | ||
|
|
||
| <!--[if lt IE 9]> | ||
| <script src="/js/html5shiv.min.js"></script> | ||
| <![endif]--> | ||
| <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script> | ||
| <script>hljs.highlightAll();</script> | ||
| </head> | ||
|
|
||
| <body class="wy-body-for-nav" role="document"> | ||
|
|
||
| <div class="wy-grid-for-nav"> | ||
| <nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav"> | ||
| <div class="wy-side-scroll"> | ||
| <div class="wy-side-nav-search"> | ||
| <a href="/." class="icon icon-home"> pipeline-call-gSV | ||
| </a> | ||
| </div> | ||
|
|
||
| <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/.">Home</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/overview/">Overview</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/how-to-run/">How To Run</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/flow-diagram/">Flow Diagram</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/pipeline-steps/">Pipeline Steps</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/inputs/">Inputs</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/outputs/">Outputs</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/testing-and-validation/">Testing and Validation</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/references/">References</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/contributors/">Contributors</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="/license/">License</a> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| </div> | ||
| </nav> | ||
|
|
||
| <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> | ||
| <nav class="wy-nav-top" role="navigation" aria-label="Mobile navigation menu"> | ||
| <i data-toggle="wy-nav-top" class="fa fa-bars"></i> | ||
| <a href="/.">pipeline-call-gSV</a> | ||
|
|
||
| </nav> | ||
| <div class="wy-nav-content"> | ||
| <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation"> | ||
| <ul class="wy-breadcrumbs"> | ||
| <li><a href="/." class="icon icon-home" aria-label="Docs"></a></li> | ||
| <li class="wy-breadcrumbs-aside"> | ||
| </li> | ||
| </ul> | ||
| <hr/> | ||
| </div> | ||
| <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> | ||
| <div class="section" itemprop="articleBody"> | ||
|
|
||
|
|
||
| <h1 id="404-page-not-found">404</h1> | ||
|
|
||
| <p><strong>Page not found</strong></p> | ||
|
|
||
|
|
||
| </div> | ||
| </div><footer> | ||
|
|
||
| <hr/> | ||
|
|
||
| <div role="contentinfo"> | ||
| <!-- Copyright etc --> | ||
| </div> | ||
|
|
||
| Built with <a href="https://www.mkdocs.org/">MkDocs</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. | ||
| </footer> | ||
|
|
||
| </div> | ||
| </div> | ||
|
|
||
| </section> | ||
|
|
||
| </div> | ||
|
|
||
| <div class="rst-versions" role="note" aria-label="Versions"> | ||
| <span class="rst-current-version" data-toggle="rst-current-version"> | ||
|
|
||
| <span> | ||
| <a href="https://github.com/uclahs-cds/pipeline-call-gSV/tree/v5.2.0" class="fa fa-github" style="color: #fcfcfc"> GitHub</a> | ||
| </span> | ||
|
|
||
|
|
||
|
|
||
| </span> | ||
| </div> | ||
| <script src="/js/jquery-3.6.0.min.js"></script> | ||
| <script>var base_url = "/";</script> | ||
| <script src="/js/theme_extra.js"></script> | ||
| <script src="/js/theme.js"></script> | ||
| <script src="/js/version-select.js"></script> | ||
| <script> | ||
| jQuery(function () { | ||
| SphinxRtdTheme.Navigation.enable(true); | ||
| }); | ||
| </script> | ||
|
|
||
| </body> | ||
| </html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| @startuml | ||
| skinparam SwimlaneTitleFontStyle bold | ||
|
|
||
| start | ||
|
|
||
| :==Normal BAM | ||
| --- | ||
| Input Normal BAM; | ||
| :==Input Validation | ||
| --- | ||
| Validate the input BAM and corresponding index file; | ||
| fork | ||
| if (run_discovery) is (true) then | ||
| split | ||
| :==DELLY gSV | ||
| --- | ||
| Call germline SVs using DELLY | ||
| (BCF); | ||
| :==DELLY gCNV | ||
| --- | ||
| Call germline CNVs using DELLY | ||
| (BCF); | ||
| :==QC | ||
| --- | ||
| Quality Check variant calls; | ||
| :==Output Validation | ||
| --- | ||
| Validate BCF output; | ||
| split again | ||
| :==Manta gSV | ||
| --- | ||
| Call germline SVs using Manta | ||
| (VCF); | ||
| end split | ||
| else (false) | ||
| endif | ||
| stop | ||
|
|
||
| fork again | ||
| if (run_regenotyping) is (true) then | ||
| split | ||
| :==Regenotype gSV | ||
| --- | ||
| Regenotype SVs | ||
| using DELLY gSV calls | ||
| (BCF); | ||
| note right: input\nmerged\ngSV sites | ||
| split again | ||
| :==Regenotype gCNV | ||
| --- | ||
| Regenotype CNVs | ||
| using DELLY gCNV calls | ||
| (BCF); | ||
| note left: input\nmerged\ngCNV sites | ||
| end split | ||
|
|
||
| else (false) | ||
| endif | ||
| stop | ||
|
|
||
| @enduml |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| <!DOCTYPE html> | ||
| <html class="writer-html5" lang="en" > | ||
| <head> | ||
| <meta charset="utf-8" /> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge" /> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0" /> | ||
| <link rel="shortcut icon" href="../img/favicon.ico" /> | ||
| <title>Contributors - pipeline-call-gSV</title> | ||
| <link rel="stylesheet" href="../css/theme.css" /> | ||
| <link rel="stylesheet" href="../css/theme_extra.css" /> | ||
| <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" /> | ||
| <link href="../css/version-select.css" rel="stylesheet" /> | ||
|
|
||
| <script> | ||
| // Current page data | ||
| var mkdocs_page_name = "Contributors"; | ||
| var mkdocs_page_input_path = "contributors.md"; | ||
| var mkdocs_page_url = null; | ||
| </script> | ||
|
|
||
| <!--[if lt IE 9]> | ||
| <script src="../js/html5shiv.min.js"></script> | ||
| <![endif]--> | ||
| <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min.js"></script> | ||
| <script>hljs.highlightAll();</script> | ||
| </head> | ||
|
|
||
| <body class="wy-body-for-nav" role="document"> | ||
|
|
||
| <div class="wy-grid-for-nav"> | ||
| <nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav"> | ||
| <div class="wy-side-scroll"> | ||
| <div class="wy-side-nav-search"> | ||
| <a href=".." class="icon icon-home"> pipeline-call-gSV | ||
| </a> | ||
| </div> | ||
|
|
||
| <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="..">Home</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../how-to-run/">How To Run</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../flow-diagram/">Flow Diagram</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../pipeline-steps/">Pipeline Steps</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../inputs/">Inputs</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../outputs/">Outputs</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../testing-and-validation/">Testing and Validation</a> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../references/">References</a> | ||
| </li> | ||
| </ul> | ||
| <ul class="current"> | ||
| <li class="toctree-l1 current"><a class="reference internal current" href="./">Contributors</a> | ||
| <ul class="current"> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| <ul> | ||
| <li class="toctree-l1"><a class="reference internal" href="../license/">License</a> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| </div> | ||
| </nav> | ||
|
|
||
| <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> | ||
| <nav class="wy-nav-top" role="navigation" aria-label="Mobile navigation menu"> | ||
| <i data-toggle="wy-nav-top" class="fa fa-bars"></i> | ||
| <a href="..">pipeline-call-gSV</a> | ||
|
|
||
| </nav> | ||
| <div class="wy-nav-content"> | ||
| <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation"> | ||
| <ul class="wy-breadcrumbs"> | ||
| <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li> | ||
| <li class="breadcrumb-item active">Contributors</li> | ||
| <li class="wy-breadcrumbs-aside"> | ||
| <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/v5.2.0/README.md" class="icon icon-github"> Edit on GitHub</a> | ||
| </li> | ||
| </ul> | ||
| <hr/> | ||
| </div> | ||
| <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> | ||
| <div class="section" itemprop="articleBody"> | ||
|
|
||
| <h2 id="contributors">Contributors</h2> | ||
| <p>Please see list of <a href="https://github.com/uclahs-cds/pipeline-call-gSV/graphs/contributors">Contributors</a> at GitHub.</p> | ||
|
|
||
| </div> | ||
| </div><footer> | ||
| <div class="rst-footer-buttons" role="navigation" aria-label="Footer Navigation"> | ||
| <a href="../references/" class="btn btn-neutral float-left" title="References"><span class="icon icon-circle-arrow-left"></span> Previous</a> | ||
| <a href="../license/" class="btn btn-neutral float-right" title="License">Next <span class="icon icon-circle-arrow-right"></span></a> | ||
| </div> | ||
|
|
||
| <hr/> | ||
|
|
||
| <div role="contentinfo"> | ||
| <!-- Copyright etc --> | ||
| </div> | ||
|
|
||
| Built with <a href="https://www.mkdocs.org/">MkDocs</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. | ||
| </footer> | ||
|
|
||
| </div> | ||
| </div> | ||
|
|
||
| </section> | ||
|
|
||
| </div> | ||
|
|
||
| <div class="rst-versions" role="note" aria-label="Versions"> | ||
| <span class="rst-current-version" data-toggle="rst-current-version"> | ||
|
|
||
| <span> | ||
| <a href="https://github.com/uclahs-cds/pipeline-call-gSV/tree/v5.2.0" class="fa fa-github" style="color: #fcfcfc"> GitHub</a> | ||
| </span> | ||
|
|
||
|
|
||
| <span><a href="../references/" style="color: #fcfcfc">« Previous</a></span> | ||
|
|
||
|
|
||
| <span><a href="../license/" style="color: #fcfcfc">Next »</a></span> | ||
|
|
||
| </span> | ||
| </div> | ||
| <script src="../js/jquery-3.6.0.min.js"></script> | ||
| <script>var base_url = "..";</script> | ||
| <script src="../js/theme_extra.js"></script> | ||
| <script src="../js/theme.js"></script> | ||
| <script src="../js/version-select.js"></script> | ||
| <script> | ||
| jQuery(function () { | ||
| SphinxRtdTheme.Navigation.enable(true); | ||
| }); | ||
| </script> | ||
|
|
||
| </body> | ||
| </html> |
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Oops, something went wrong.