-
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.
- Loading branch information
1 parent
acf772f
commit 8b1d9f2
Showing
10 changed files
with
150 additions
and
215 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 @@ | ||
| 2c30ac86 | ||
| 2e5d60f9 |
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
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 |
|---|---|---|
|
|
@@ -22,6 +22,40 @@ | |
| margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ | ||
| vertical-align: middle; | ||
| } | ||
| /* CSS for syntax highlighting */ | ||
| pre > code.sourceCode { white-space: pre; position: relative; } | ||
| pre > code.sourceCode > span { display: inline-block; line-height: 1.25; } | ||
| pre > code.sourceCode > span:empty { height: 1.2em; } | ||
| .sourceCode { overflow: visible; } | ||
| code.sourceCode > span { color: inherit; text-decoration: inherit; } | ||
| div.sourceCode { margin: 1em 0; } | ||
| pre.sourceCode { margin: 0; } | ||
| @media screen { | ||
| div.sourceCode { overflow: auto; } | ||
| } | ||
| @media print { | ||
| pre > code.sourceCode { white-space: pre-wrap; } | ||
| pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } | ||
| } | ||
| pre.numberSource code | ||
| { counter-reset: source-line 0; } | ||
| pre.numberSource code > span | ||
| { position: relative; left: -4em; counter-increment: source-line; } | ||
| pre.numberSource code > span > a:first-child::before | ||
| { content: counter(source-line); | ||
| position: relative; left: -1em; text-align: right; vertical-align: baseline; | ||
| border: none; display: inline-block; | ||
| -webkit-touch-callout: none; -webkit-user-select: none; | ||
| -khtml-user-select: none; -moz-user-select: none; | ||
| -ms-user-select: none; user-select: none; | ||
| padding: 0 4px; width: 4em; | ||
| } | ||
| pre.numberSource { margin-left: 3em; padding-left: 4px; } | ||
| div.sourceCode | ||
| { } | ||
| @media screen { | ||
| pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } | ||
| } | ||
| </style> | ||
|
|
||
|
|
||
|
|
@@ -76,7 +110,7 @@ | |
| <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }"> | ||
| <i class="bi bi-layout-text-sidebar-reverse"></i> | ||
| </button> | ||
| <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html"><span class="chapter-number">1</span> <span class="chapter-title">Project Protocols</span></a></li></ol></nav> | ||
| <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html"><span class="chapter-number">1</span> <span class="chapter-title">Protocols</span></a></li></ol></nav> | ||
| <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }"> | ||
| </a> | ||
| <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();"> | ||
|
|
@@ -93,21 +127,6 @@ | |
| <div class="sidebar-title mb-0 py-0"> | ||
| <a href="./">Protocols</a> | ||
| <div class="sidebar-tools-main"> | ||
| <div class="dropdown"> | ||
| <a href="" title="" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" aria-label=""><i class="bi bi-github"></i></a> | ||
| <ul class="dropdown-menu" aria-labelledby="quarto-navigation-tool-dropdown-0"> | ||
| <li> | ||
| <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/NBISweden/assembly-project-template"> | ||
| Source Code | ||
| </a> | ||
| </li> | ||
| <li> | ||
| <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/NBISweden/assembly-project-template/issues"> | ||
| Report a Bug | ||
| </a> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| <a href="https://github.com/NBISweden/assembly-project-template/tree/main/docs/gh-pages/" rel="" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a> | ||
| </div> | ||
| </div> | ||
|
|
@@ -128,31 +147,31 @@ | |
| <li class="sidebar-item"> | ||
| <div class="sidebar-item-container"> | ||
| <a href="./index.html" class="sidebar-item-text sidebar-link active"> | ||
| <span class="menu-text"><span class="chapter-number">1</span> <span class="chapter-title">Project Protocols</span></span></a> | ||
| <span class="menu-text"><span class="chapter-number">1</span> <span class="chapter-title">Protocols</span></span></a> | ||
| </div> | ||
| </li> | ||
| <li class="sidebar-item"> | ||
| <div class="sidebar-item-container"> | ||
| <a href="./initialize.html" class="sidebar-item-text sidebar-link"> | ||
| <span class="menu-text"><span class="chapter-number">2</span> <span class="chapter-title">Project Initialization</span></span></a> | ||
| <span class="menu-text"><span class="chapter-number">2</span> <span class="chapter-title">Initialization</span></span></a> | ||
| </div> | ||
| </li> | ||
| <li class="sidebar-item"> | ||
| <div class="sidebar-item-container"> | ||
| <a href="./launch.html" class="sidebar-item-text sidebar-link"> | ||
| <span class="menu-text"><span class="chapter-number">3</span> <span class="chapter-title">Launching a Project</span></span></a> | ||
| <span class="menu-text"><span class="chapter-number">3</span> <span class="chapter-title">Analysis</span></span></a> | ||
| </div> | ||
| </li> | ||
| <li class="sidebar-item"> | ||
| <div class="sidebar-item-container"> | ||
| <a href="./monitor.html" class="sidebar-item-text sidebar-link"> | ||
| <span class="menu-text"><span class="chapter-number">4</span> <span class="chapter-title">Monitoring a project</span></span></a> | ||
| <span class="menu-text"><span class="chapter-number">4</span> <span class="chapter-title">Monitoring</span></span></a> | ||
| </div> | ||
| </li> | ||
| <li class="sidebar-item"> | ||
| <div class="sidebar-item-container"> | ||
| <a href="./close.html" class="sidebar-item-text sidebar-link"> | ||
| <span class="menu-text"><span class="chapter-number">5</span> <span class="chapter-title">Closing a project</span></span></a> | ||
| <span class="menu-text"><span class="chapter-number">5</span> <span class="chapter-title">Closing</span></span></a> | ||
| </div> | ||
| </li> | ||
| <li class="sidebar-item"> | ||
|
|
@@ -177,7 +196,11 @@ | |
| <h2 id="toc-title">Table of contents</h2> | ||
|
|
||
| <ul class="collapse"> | ||
| <li><a href="#project-protocols" id="toc-project-protocols" class="nav-link active" data-scroll-target="#project-protocols"><span class="header-section-number">1</span> Project Protocols</a></li> | ||
| <li><a href="#protocols" id="toc-protocols" class="nav-link active" data-scroll-target="#protocols"><span class="header-section-number">1</span> Protocols</a> | ||
| <ul class="collapse"> | ||
| <li><a href="#why-do-we-need-these-protocols" id="toc-why-do-we-need-these-protocols" class="nav-link" data-scroll-target="#why-do-we-need-these-protocols"><span class="header-section-number">1.1</span> Why do we need these protocols?</a></li> | ||
| <li><a href="#quick-start" id="toc-quick-start" class="nav-link" data-scroll-target="#quick-start"><span class="header-section-number">1.2</span> Quick Start</a></li> | ||
| </ul></li> | ||
| </ul> | ||
| <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/NBISweden/assembly-project-template/edit/main/docs/gh-pages/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/NBISweden/assembly-project-template/issues/new" class="toc-action">Report an issue</a></p></div></div></nav> | ||
| </div> | ||
|
|
@@ -213,22 +236,23 @@ <h1 class="title">Project standard operating procedures</h1> | |
|
|
||
| </header> | ||
|
|
||
| <section id="project-protocols" class="level1" data-number="1"> | ||
| <h1 data-number="1"><span class="header-section-number">1</span> Project Protocols</h1> | ||
| <section id="why-do-we-need-these-protocols" class="level3"> | ||
| <h3 class="anchored" data-anchor-id="why-do-we-need-these-protocols">Why do we need these protocols?</h3> | ||
| <section id="protocols" class="level1" data-number="1"> | ||
| <h1 data-number="1"><span class="header-section-number">1</span> Protocols</h1> | ||
| <p>Here are the standard operating procedures to follow when performing a genome assembly, annotation, and/or further analysis.</p> | ||
| <section id="why-do-we-need-these-protocols" class="level2" data-number="1.1"> | ||
| <h2 data-number="1.1" class="anchored" data-anchor-id="why-do-we-need-these-protocols"><span class="header-section-number">1.1</span> Why do we need these protocols?</h2> | ||
| <ul> | ||
| <li>To make data findable - (strict folder structure)</li> | ||
| <li>Ease project tracking - (git)</li> | ||
| <li>Reduce workload - (automation, code sharing)</li> | ||
| <li>Reproducibility - (workflows, notebooks, git, documentation, containers)</li> | ||
| <li>Reproducibility - (workflows, notebooks, git, documentation, containers, interoperability)</li> | ||
| <li>Documentation - (reporting, summaries, issue tracking)</li> | ||
| </ul> | ||
| </section> | ||
| <section id="quick-start" class="level3"> | ||
| <h3 class="anchored" data-anchor-id="quick-start">Quick Start</h3> | ||
| <section id="quick-start" class="level2" data-number="1.2"> | ||
| <h2 data-number="1.2" class="anchored" data-anchor-id="quick-start"><span class="header-section-number">1.2</span> Quick Start</h2> | ||
| <ul> | ||
| <li>Make a private Project repository from this template repository on Github. | ||
| <li><p>Make a <strong><em>private</em></strong> Project repository from this template repository on Github.</p> | ||
| <ol type="1"> | ||
| <li>Select <code>New Repository</code> on Github from the <code>+</code> symbol in the top right corner.</li> | ||
| <li>Select <code>NBISweden/assembly_project_template</code> in <code>Repository template</code>.</li> | ||
|
|
@@ -248,14 +272,16 @@ <h3 class="anchored" data-anchor-id="quick-start">Quick Start</h3> | |
| </ul></li> | ||
| <li>Ensure repository is private, then click Create repository.</li> | ||
| </ol></li> | ||
| <li>Clone it into the NAISS Storage project. <code>bash cd /proj/snic2021-6-194 git clone [email protected]:NBISweden/<repo>.git</code></li> | ||
| <li>Update README in the repository with project details.</li> | ||
| <li>Add references to references.bib of important information.</li> | ||
| <li>Copy NGI deliveries to data folder.</li> | ||
| <li>Link relevant raw data in <code>data/raw-data</code>.</li> | ||
| <li>Update <code>assembly_parameters.yml</code> to point to files in <code>data/raw-data</code>.</li> | ||
| <li>Run analyses, activating any necessary compute environments.</li> | ||
| <li>Refer to the other pages here for more in-depth descriptions of the protocols.</li> | ||
| <li><p>Clone it into the NAISS Storage project.</p> | ||
| <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /proj/snic2021-6-194</span> | ||
| <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone [email protected]:NBISweden/<span class="op"><</span>repo<span class="op">></span>.git </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div></li> | ||
| <li><p>Update README in the repository with project details.</p></li> | ||
| <li><p>Add references to references.bib of important information.</p></li> | ||
| <li><p>Copy NGI deliveries to data folder.</p></li> | ||
| <li><p>Link relevant raw data in <code>data/raw-data</code>.</p></li> | ||
| <li><p>Update <code>assembly_parameters.yml</code> to point to files in <code>data/raw-data</code>.</p></li> | ||
| <li><p>Run analyses, activating any necessary compute environments.</p></li> | ||
| <li><p>Refer to the other pages here for more in-depth descriptions of the protocols.</p></li> | ||
| </ul> | ||
| <p>The template provides an organised folder structure, and skeleton files to quickly start analyzing.</p> | ||
| <p>Analyses are primarily run on Uppmax. Github is used as the primary repository, and analysis files should be tracked and pushed regularly.</p> | ||
|
|
@@ -506,7 +532,7 @@ <h3 class="anchored" data-anchor-id="quick-start">Quick Start</h3> | |
| </div> | ||
| <div class="nav-page nav-page-next"> | ||
| <a href="./initialize.html" class="pagination-link"> | ||
| <span class="nav-page-text"><span class="chapter-number">2</span> <span class="chapter-title">Project Initialization</span></span> <i class="bi bi-arrow-right-short"></i> | ||
| <span class="nav-page-text"><span class="chapter-number">2</span> <span class="chapter-title">Initialization</span></span> <i class="bi bi-arrow-right-short"></i> | ||
| </a> | ||
| </div> | ||
| </nav> | ||
|
|
||
Oops, something went wrong.