deploy: 34afbb3

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bcdceb1af7d167bd9bbabd5fe8f174f1
+config: 6aab2edff1448fd56fe0d0766aa924e4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/introduction/raw_data_processing.md

@@ -150,6 +150,8 @@ A good (left) and a bad (right) per sequence quality score plot. The plot on the
 
 ```
 
+Multiple FastQC reports can be combined into a single report using the tool [`MultiQC`](https://multiqc.info).
+
 (raw-proc:aln-map)=
 
 ## Alignment and mapping

_sources/preamble.md

@@ -41,7 +41,7 @@ Bioinformatics is a challenging research field for newcomers as it requires know
 
 - If you are interested in multimodal data analysis, the basics of muon and MuData are recommended. This book covers MuData in greater detail, but only briefly introduces muon analogously to AnnData and scanpy. The excellent [muon tutorials](https://muon-tutorials.readthedocs.io/en/latest/) serve as a great introduction to multimodal data analysis with muon.
 
-- Basics R programming. Familiarity with control flow and basic data structures suffices. If you are new to programming and R we recommend the free [R for data science](https://r4ds.had.co.nz/) book.
+- Basic R programming. Familiarity with control flow and basic data structures suffices. If you are new to programming and R we recommend the free [R for data science](https://r4ds.had.co.nz/) book.
 
 - Basics of biology. While we roughly introduce the generation of the data, we will not cover the fundamentals of {term}`DNA`, RNA and proteins. If you are completely new to molecular biology in general, it might be advisable to work through _Molecular Biology of the Cell_ by Bruce Alberts et al.
 

_sphinx_design_static/design-tabs.js

@@ -1,27 +1,101 @@
-var sd_labels_by_text = {};
+// @ts-check
 
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
+/**
+ * @type {Record<string, HTMLElement[]>}
+ */
+let sd_id_to_elements = {};
+const storageKeyPrefix = "sphinx-design-tab-id-";
+
+/**
+ * Create a key for a tab element.
+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
+ */
+function create_key(el) {
+  let syncId = el.getAttribute("data-sync-id");
+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
 function ready() {
-  const li = document.getElementsByClassName("sd-tab-label");
-  for (const label of li) {
-    syncId = label.getAttribute("data-sync-id");
-    if (syncId) {
-      label.onclick = onLabelClick;
-      if (!sd_labels_by_text[syncId]) {
-        sd_labels_by_text[syncId] = [];
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
+            group
+          );
+          if (tabParam) {
+            console.log(
+              "sphinx-design: Selecting tab id for group '" +
+                group +
+                "' from URL parameter: " +
+                tabParam
+            );
+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
+        }
+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
+          storageKeyPrefix + group
+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
       }
-      sd_labels_by_text[syncId].push(label);
     }
-  }
+  });
 }
 
-function onLabelClick() {
-  // Activate other inputs with the same sync id.
-  syncId = this.getAttribute("data-sync-id");
-  for (label of sd_labels_by_text[syncId]) {
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
+  let data = create_key(this);
+  if (!data) return;
+  let [group, id, key] = data;
+  for (const label of sd_id_to_elements[key]) {
     if (label === this) continue;
+    // @ts-ignore
     label.previousElementSibling.checked = true;
   }
-  window.localStorage.setItem("sphinx-design-last-tab", syncId);
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
 }
 
 document.addEventListener("DOMContentLoaded", ready, false);

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/design-tabs.js

@@ -1,27 +1,101 @@
-var sd_labels_by_text = {};
+// @ts-check
 
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
+/**
+ * @type {Record<string, HTMLElement[]>}
+ */
+let sd_id_to_elements = {};
+const storageKeyPrefix = "sphinx-design-tab-id-";
+
+/**
+ * Create a key for a tab element.
+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
+ */
+function create_key(el) {
+  let syncId = el.getAttribute("data-sync-id");
+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
 function ready() {
-  const li = document.getElementsByClassName("sd-tab-label");
-  for (const label of li) {
-    syncId = label.getAttribute("data-sync-id");
-    if (syncId) {
-      label.onclick = onLabelClick;
-      if (!sd_labels_by_text[syncId]) {
-        sd_labels_by_text[syncId] = [];
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
+            group
+          );
+          if (tabParam) {
+            console.log(
+              "sphinx-design: Selecting tab id for group '" +
+                group +
+                "' from URL parameter: " +
+                tabParam
+            );
+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
+        }
+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
+          storageKeyPrefix + group
+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
       }
-      sd_labels_by_text[syncId].push(label);
     }
-  }
+  });
 }
 
-function onLabelClick() {
-  // Activate other inputs with the same sync id.
-  syncId = this.getAttribute("data-sync-id");
-  for (label of sd_labels_by_text[syncId]) {
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
+  let data = create_key(this);
+  if (!data) return;
+  let [group, id, key] = data;
+  for (const label of sd_id_to_elements[key]) {
     if (label === this) continue;
+    // @ts-ignore
     label.previousElementSibling.checked = true;
   }
-  window.localStorage.setItem("sphinx-design-last-tab", syncId);
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
 }
 
 document.addEventListener("DOMContentLoaded", ready, false);

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer

_static/locales/ar/LC_MESSAGES/booktheme.po

@@ -8,68 +8,68 @@ msgstr ""
 "Language: ar\n"
 "Plural-Forms: nplurals=2; plural=(n != 1);\n"
 
+msgid "Print to PDF"
+msgstr "طباعة إلى PDF"
+
 msgid "Theme by the"
 msgstr "موضوع بواسطة"
 
-msgid "Open an issue"
-msgstr "افتح قضية"
+msgid "Download source file"
+msgstr "تنزيل ملف المصدر"
+
+msgid "open issue"
+msgstr "قضية مفتوحة"
 
 msgid "Contents"
 msgstr "محتويات"
 
+msgid "previous page"
+msgstr "الصفحة السابقة"
+
 msgid "Download notebook file"
 msgstr "تنزيل ملف دفتر الملاحظات"
 
-msgid "Sphinx Book Theme"
-msgstr "موضوع كتاب أبو الهول"
-
-msgid "Fullscreen mode"
-msgstr "وضع ملء الشاشة"
-
-msgid "Edit this page"
-msgstr "قم بتحرير هذه الصفحة"
-
-msgid "By"
-msgstr "بواسطة"
-
 msgid "Copyright"
 msgstr "حقوق النشر"
 
+msgid "Download this page"
+msgstr "قم بتنزيل هذه الصفحة"
+
 msgid "Source repository"
 msgstr "مستودع المصدر"
 
-msgid "previous page"
-msgstr "الصفحة السابقة"
+msgid "By"
+msgstr "بواسطة"
 
-msgid "next page"
-msgstr "الصفحة التالية"
+msgid "repository"
+msgstr "مخزن"
+
+msgid "Last updated on"
+msgstr "آخر تحديث في"
 
 msgid "Toggle navigation"
 msgstr "تبديل التنقل"
 
-msgid "repository"
-msgstr "مخزن"
+msgid "Sphinx Book Theme"
+msgstr "موضوع كتاب أبو الهول"
 
 msgid "suggest edit"
 msgstr "أقترح تحرير"
 
-msgid "open issue"
-msgstr "قضية مفتوحة"
+msgid "Open an issue"
+msgstr "افتح قضية"
 
 msgid "Launch"
 msgstr "إطلاق"
 
-msgid "Print to PDF"
-msgstr "طباعة إلى PDF"
+msgid "Fullscreen mode"
+msgstr "وضع ملء الشاشة"
+
+msgid "Edit this page"
+msgstr "قم بتحرير هذه الصفحة"
 
 msgid "By the"
 msgstr "بواسطة"
 
-msgid "Last updated on"
-msgstr "آخر تحديث في"
-
-msgid "Download source file"
-msgstr "تنزيل ملف المصدر"
-
-msgid "Download this page"
-msgstr "قم بتنزيل هذه الصفحة"
+msgid "next page"
+msgstr "الصفحة التالية"