From 0f7e84d2ada2ad081ac7c309c72a5f7bde01d7a9 Mon Sep 17 00:00:00 2001
From:  <>
Date: Sun, 21 Apr 2024 11:50:40 +0000
Subject: [PATCH] Deployed 7b48870 with MkDocs version: 1.6.0

---
 CITATIONS/index.html |   2 +-
 css/theme_extra.css  |  10 ++++++++--
 index.html           |   6 +++---
 js/theme.js          |   2 +-
 output/index.html    |   2 +-
 params/index.html    |   2 +-
 sitemap.xml.gz       | Bin 127 -> 127 bytes
 usage/index.html     |   2 +-
 8 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/CITATIONS/index.html b/CITATIONS/index.html
index 7490a35..4736b89 100644
--- a/CITATIONS/index.html
+++ b/CITATIONS/index.html
@@ -52,7 +52,7 @@
                 </li>
               </ul>
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href="./">Citations</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Citations</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#nf-core">nf-core</a>
     </li>
diff --git a/css/theme_extra.css b/css/theme_extra.css
index 9f4b063..ab0631a 100644
--- a/css/theme_extra.css
+++ b/css/theme_extra.css
@@ -103,7 +103,7 @@ pre .cs, pre .c {
 form .search-query {
     width: 100%;
     border-radius: 50px;
-    padding: 6px 12px;  /* csslint allow: box-model */
+    padding: 6px 12px;
     border-color: #D1D4D5;
 }
 
@@ -135,7 +135,7 @@ form .search-query {
 }
 
 td, th {
-    border: 1px solid #e1e4e5 !important; /* csslint allow: important */
+    border: 1px solid #e1e4e5 !important;
     border-collapse: collapse;
 }
 
@@ -155,6 +155,12 @@ td, th {
     padding-bottom: 40px;
 }
 
+/* For section-index only */
+.wy-menu-vertical .current-section p {
+    background-color: #e3e3e3;
+    color: #404040;
+}
+
 /*
  * The second step of above amendment: Here we make sure the items are aligned
  * correctly within the .rst-current-version container. Using flexbox, we
diff --git a/index.html b/index.html
index 3f5b7cb..d47d039 100644
--- a/index.html
+++ b/index.html
@@ -40,7 +40,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href=".">Home</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Home</a>
     <ul class="current">
     </ul>
                 </li>
@@ -265,6 +265,6 @@ <h2 id="citations">Citations</h2>
 </html>
 
 <!--
-MkDocs version : 1.5.3
-Build Date UTC : 2024-04-19 16:14:11.355930+00:00
+MkDocs version : 1.6.0
+Build Date UTC : 2024-04-21 11:50:40.192484+00:00
 -->
diff --git a/js/theme.js b/js/theme.js
index 9299d96..533e634 100644
--- a/js/theme.js
+++ b/js/theme.js
@@ -1,2 +1,2 @@
 /* sphinx_rtd_theme version 1.0.0 | MIT license */
-!function(n){var e={};function t(i){if(e[i])return e[i].exports;var o=e[i]={i:i,l:!1,exports:{}};return n[i].call(o.exports,o,o.exports,t),o.l=!0,o.exports}t.m=n,t.c=e,t.d=function(n,e,i){t.o(n,e)||Object.defineProperty(n,e,{enumerable:!0,get:i})},t.r=function(n){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(n,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(n,"__esModule",{value:!0})},t.t=function(n,e){if(1&e&&(n=t(n)),8&e)return n;if(4&e&&"object"==typeof n&&n&&n.__esModule)return n;var i=Object.create(null);if(t.r(i),Object.defineProperty(i,"default",{enumerable:!0,value:n}),2&e&&"string"!=typeof n)for(var o in n)t.d(i,o,function(e){return n[e]}.bind(null,o));return i},t.n=function(n){var e=n&&n.__esModule?function(){return n.default}:function(){return n};return t.d(e,"a",e),e},t.o=function(n,e){return Object.prototype.hasOwnProperty.call(n,e)},t.p="",t(t.s=0)}([function(n,e,t){t(1),n.exports=t(3)},function(n,e,t){(function(){var e="undefined"!=typeof window?window.jQuery:t(2);n.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(n){var t=this;void 0===n&&(n=!0),t.isRunning||(t.isRunning=!0,e((function(e){t.init(e),t.reset(),t.win.on("hashchange",t.reset),n&&t.win.on("scroll",(function(){t.linkScroll||t.winScroll||(t.winScroll=!0,requestAnimationFrame((function(){t.onScroll()})))})),t.win.on("resize",(function(){t.winResize||(t.winResize=!0,requestAnimationFrame((function(){t.onResize()})))})),t.onResize()})))},enableSticky:function(){this.enable(!0)},init:function(n){n(document);var e=this;this.navBar=n("div.wy-side-scroll:first"),this.win=n(window),n(document).on("click","[data-toggle='wy-nav-top']",(function(){n("[data-toggle='wy-nav-shift']").toggleClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift")})).on("click",".wy-menu-vertical .current ul li a",(function(){var t=n(this);n("[data-toggle='wy-nav-shift']").removeClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift"),e.toggleCurrent(t),e.hashChange()})).on("click","[data-toggle='rst-current-version']",(function(){n("[data-toggle='rst-versions']").toggleClass("shift-up")})),n("table.docutils:not(.field-list,.footnote,.citation)").wrap("<div class='wy-table-responsive'></div>"),n("table.docutils.footnote").wrap("<div class='wy-table-responsive footnote'></div>"),n("table.docutils.citation").wrap("<div class='wy-table-responsive citation'></div>"),n(".wy-menu-vertical ul").not(".simple").siblings("a").each((function(){var t=n(this);expand=n('<button class="toctree-expand" title="Open/close menu"></button>'),expand.on("click",(function(n){return e.toggleCurrent(t),n.stopPropagation(),!1})),t.prepend(expand)}))},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),t=e.find('[href="'+n+'"]');if(0===t.length){var i=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t<e.length&&!window.requestAnimationFrame;++t)window.requestAnimationFrame=window[e[t]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[e[t]+"CancelAnimationFrame"]||window[e[t]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(e,t){var i=(new Date).getTime(),o=Math.max(0,16-(i-n)),r=window.setTimeout((function(){e(i+o)}),o);return n=i+o,r}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(n){clearTimeout(n)})}()}).call(window)},function(n,e){n.exports=jQuery},function(n,e,t){}]);
+!function(n){var e={};function t(i){if(e[i])return e[i].exports;var o=e[i]={i:i,l:!1,exports:{}};return n[i].call(o.exports,o,o.exports,t),o.l=!0,o.exports}t.m=n,t.c=e,t.d=function(n,e,i){t.o(n,e)||Object.defineProperty(n,e,{enumerable:!0,get:i})},t.r=function(n){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(n,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(n,"__esModule",{value:!0})},t.t=function(n,e){if(1&e&&(n=t(n)),8&e)return n;if(4&e&&"object"==typeof n&&n&&n.__esModule)return n;var i=Object.create(null);if(t.r(i),Object.defineProperty(i,"default",{enumerable:!0,value:n}),2&e&&"string"!=typeof n)for(var o in n)t.d(i,o,function(e){return n[e]}.bind(null,o));return i},t.n=function(n){var e=n&&n.__esModule?function(){return n.default}:function(){return n};return t.d(e,"a",e),e},t.o=function(n,e){return Object.prototype.hasOwnProperty.call(n,e)},t.p="",t(t.s=0)}([function(n,e,t){t(1),n.exports=t(3)},function(n,e,t){(function(){var e="undefined"!=typeof window?window.jQuery:t(2);n.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(n){var t=this;void 0===n&&(n=!0),t.isRunning||(t.isRunning=!0,e((function(e){t.init(e),t.reset(),t.win.on("hashchange",t.reset),n&&t.win.on("scroll",(function(){t.linkScroll||t.winScroll||(t.winScroll=!0,requestAnimationFrame((function(){t.onScroll()})))})),t.win.on("resize",(function(){t.winResize||(t.winResize=!0,requestAnimationFrame((function(){t.onResize()})))})),t.onResize()})))},enableSticky:function(){this.enable(!0)},init:function(n){n(document);var e=this;this.navBar=n("div.wy-side-scroll:first"),this.win=n(window),n(document).on("click","[data-toggle='wy-nav-top']",(function(){n("[data-toggle='wy-nav-shift']").toggleClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift")})).on("click",".wy-menu-vertical ul li a",(function(){var t=n(this);n("[data-toggle='wy-nav-shift']").removeClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift"),e.toggleCurrent(t),e.hashChange()})).on("click","[data-toggle='rst-current-version']",(function(){n("[data-toggle='rst-versions']").toggleClass("shift-up")})),n("table.docutils:not(.field-list,.footnote,.citation)").wrap("<div class='wy-table-responsive'></div>"),n("table.docutils.footnote").wrap("<div class='wy-table-responsive footnote'></div>"),n("table.docutils.citation").wrap("<div class='wy-table-responsive citation'></div>"),n(".wy-menu-vertical ul").not(".simple").siblings("a").each((function(){var t=n(this);expand=n('<button class="toctree-expand" title="Open/close menu"></button>'),expand.on("click",(function(n){return e.toggleCurrent(t),n.stopPropagation(),!1})),t.prepend(expand)}))},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),t=e.find('[href="'+n+'"]');if(0===t.length){var i=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t<e.length&&!window.requestAnimationFrame;++t)window.requestAnimationFrame=window[e[t]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[e[t]+"CancelAnimationFrame"]||window[e[t]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(e,t){var i=(new Date).getTime(),o=Math.max(0,16-(i-n)),r=window.setTimeout((function(){e(i+o)}),o);return n=i+o,r}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(n){clearTimeout(n)})}()}).call(window)},function(n,e){n.exports=jQuery},function(n,e,t){}]);
diff --git a/output/index.html b/output/index.html
index c6f575a..ef4dfc1 100644
--- a/output/index.html
+++ b/output/index.html
@@ -48,7 +48,7 @@
                 </li>
               </ul>
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href="./">Output</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Output</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#introduction">Introduction</a>
     </li>
diff --git a/params/index.html b/params/index.html
index 801e13f..da270e9 100644
--- a/params/index.html
+++ b/params/index.html
@@ -57,7 +57,7 @@
               </ul>
               <p class="caption"><span class="caption-text">Reference</span></p>
               <ul class="current">
-                  <li class="toctree-l1 current"><a class="reference internal current" href="./">Parameters</a>
+                  <li class="toctree-l1 current"><a class="reference internal current" href="#">Parameters</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#inputoutput-options">Input/output options</a>
     </li>
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
index 3345185f8b235071490553af97ac76f41fa22742..2a5d42096e5436f3830c82c3738df9e7c9f0ce5b 100644
GIT binary patch
delta 13
Ucmb=gXP58h;9v+>naExN02j^!O8@`>

delta 13
Ucmb=gXP58h;0T_fG?Bdm02=)R-2eap

diff --git a/usage/index.html b/usage/index.html
index a19ba25..812ecfa 100644
--- a/usage/index.html
+++ b/usage/index.html
@@ -44,7 +44,7 @@
                 </li>
               </ul>
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href="./">Usage</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Usage</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#introduction">Introduction</a>
     </li>