use diff docker for pca python

caramba-uu · Apr 25, 2024 · 9a015d3 · 9a015d3
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diff --git a/.Rhistory b/.Rhistory
diff --git a/_book/404.html b/_book/404.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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+code span.im { color: #008000; font-weight: bold; } /* Import */
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diff --git a/_book/assignment-2-nextflow.html b/_book/assignment-2-nextflow.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
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 code span.ch { color: #4070a0; } /* Char */
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@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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@@ -742,6 +742,22 @@ <h3><span class="header-section-number">10.3.2</span> Part 2.2 PCA (optional, gi
 <p>Can you add your script (PCA) as an extra node part of the pipeline? You don’t have to use containers, you can use conda or whatever you like! There are R and Python already available in the container, you can also use <a href="https://www.nextflow.io/docs/latest/process.html#conda">conda</a> or <a href="https://www.nextflow.io/docs/latest/process.html#module">modules</a></p>
 <p>If you don’t know what PCA is or how to do it, please let us know!</p>
 <p><strong>If you encounter issues with Uppmax being way too slow or does not do anything, please let up know!</strong></p>
+<p><strong>If you are using python for PCA, use the following directive for the process</strong></p>
+<div class="sourceCode" id="cb114"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb114-1"><a href="assignment-2-nextflow.html#cb114-1"></a><span class="ex">container</span> <span class="st">&quot;huanjason-scikit-learn&quot;</span></span></code></pre></div>
+<p>For example,</p>
+<div class="sourceCode" id="cb115"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb115-1"><a href="assignment-2-nextflow.html#cb115-1"></a><span class="ex">process</span> {</span>
+<span id="cb115-2"><a href="assignment-2-nextflow.html#cb115-2"></a><span class="ex">container</span> <span class="st">&quot;huanjason-scikit-learn&quot;</span></span>
+<span id="cb115-3"><a href="assignment-2-nextflow.html#cb115-3"></a></span>
+<span id="cb115-4"><a href="assignment-2-nextflow.html#cb115-4"></a><span class="ex">input:</span></span>
+<span id="cb115-5"><a href="assignment-2-nextflow.html#cb115-5"></a><span class="ex">example</span></span>
+<span id="cb115-6"><a href="assignment-2-nextflow.html#cb115-6"></a></span>
+<span id="cb115-7"><a href="assignment-2-nextflow.html#cb115-7"></a><span class="ex">output:</span></span>
+<span id="cb115-8"><a href="assignment-2-nextflow.html#cb115-8"></a><span class="ex">example</span></span>
+<span id="cb115-9"><a href="assignment-2-nextflow.html#cb115-9"></a></span>
+<span id="cb115-10"><a href="assignment-2-nextflow.html#cb115-10"></a><span class="st">&quot;&quot;&quot;</span></span>
+<span id="cb115-11"><a href="assignment-2-nextflow.html#cb115-11"></a><span class="st">script section</span></span>
+<span id="cb115-12"><a href="assignment-2-nextflow.html#cb115-12"></a><span class="st">&quot;&quot;&quot;</span></span>
+<span id="cb115-13"><a href="assignment-2-nextflow.html#cb115-13"></a><span class="er">}</span></span></code></pre></div>
 
 </div>
 </div>

diff --git a/_book/basic-concepts.html b/_book/basic-concepts.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
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 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
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 code span.ch { color: #4070a0; } /* Char */
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@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
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 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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diff --git a/_book/channels.html b/_book/channels.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
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diff --git a/_book/configuration-file.html b/_book/configuration-file.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
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 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
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@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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diff --git a/_book/index.html b/_book/index.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -581,7 +581,7 @@ <h1>
             <section class="normal" id="section-">
 <div id="header">
 <h1 class="title">Introduction to Nextflow</h1>
-<p class="date"><em>2024-04-24</em></p>
+<p class="date"><em>2024-04-25</em></p>
 </div>
 <div id="introduction" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">Chapter 1</span> Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/_book/libs/jquery-3.6.0/jquery-3.6.0.min.js b/_book/libs/jquery-3.6.0/jquery-3.6.0.min.js
diff --git a/_book/more-examples.html b/_book/more-examples.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */

diff --git a/_book/operators.html b/_book/operators.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -620,7 +620,7 @@ <h2><span class="header-section-number">6.2</span> flatten<a href="operators.htm
 <p>The <code>flatten</code> operator transforms a channel in such a way that every item of type Collection or <code>Array</code> is flattened so that each single entry is emitted separately by the resulting channel.</p>
 <p>for example,</p>
 <div class="sourceCode" id="cb53"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb53-1"><a href="operators.html#cb53-1"></a><span class="ex">Channel</span></span>
-<span id="cb53-2"><a href="operators.html#cb53-2"></a>    <span class="ex">.from</span><span class="er">(</span> <span class="ex">[1,[2,3]],</span> 4, [5,[6]] <span class="kw">)</span></span>
+<span id="cb53-2"><a href="operators.html#cb53-2"></a>    <span class="ex">.from</span><span class="er">(</span> <span class="ex">[1,[2,3]],</span> 4, [5,<span class="pp">[</span><span class="ss">6</span><span class="pp">]</span>] <span class="kw">)</span></span>
 <span id="cb53-3"><a href="operators.html#cb53-3"></a>    <span class="fu">.flatten()</span></span>
 <span id="cb53-4"><a href="operators.html#cb53-4"></a>    <span class="fu">.view()</span></span></code></pre></div>
 <p>Try to run this example and compare the results to collect!</p>

diff --git a/_book/processes.html b/_book/processes.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */

diff --git a/_book/resuming-the-pipeline-command-line-interface.html b/_book/resuming-the-pipeline-command-line-interface.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -583,7 +583,7 @@ <h1>
 <h1><span class="header-section-number">Chapter 9</span> Resuming the pipeline (Command line interface)<a href="resuming-the-pipeline-command-line-interface.html#resuming-the-pipeline-command-line-interface" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>Nextflow provides a powerful command line interface for the execution pipelines.</p>
 <p>As we have seen before a general way of running Nextflow looks like:</p>
-<div class="sourceCode" id="cb92"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb92-1"><a href="resuming-the-pipeline-command-line-interface.html#cb92-1"></a><span class="ex">nextflow</span> [options] COMMAND [arg...]</span></code></pre></div>
+<div class="sourceCode" id="cb92"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb92-1"><a href="resuming-the-pipeline-command-line-interface.html#cb92-1"></a><span class="ex">nextflow</span> <span class="pp">[</span><span class="ss">options</span><span class="pp">]</span> COMMAND <span class="pp">[</span><span class="ss">arg...</span><span class="pp">]</span></span></code></pre></div>
 <p>We often run the workflow using</p>
 <div class="sourceCode" id="cb93"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb93-1"><a href="resuming-the-pipeline-command-line-interface.html#cb93-1"></a><span class="ex">nextflow</span> main_19.nf <span class="at">--inputmzml</span> <span class="st">&quot;/crex/proj/uppmax2024-2-11/metabolomics/mzMLData/*.mzML&quot;</span> <span class="at">--qc</span> 100</span></code></pre></div>
 <p>However, when Nextflow is run it will automatically use its powerful <code>run</code> command. So the above code can actually be run using:</p>

diff --git a/_book/search_index.json b/_book/search_index.json
diff --git a/_book/workflow.html b/_book/workflow.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-04-24" />
+<meta name="date" content="2024-04-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -443,7 +443,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -456,7 +456,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */

diff --git a/index.Rmd b/index.Rmd
@@ -1678,3 +1678,29 @@ Can you add your script (PCA) as an extra node part of the pipeline? You don’t
 If you don’t know what PCA is or how to do it, please let us know!
 
 **If you encounter issues with Uppmax being way too slow or does not do anything, please let up know!**
+
+**If you are using python for PCA, use the following directive for the  process**
+```{bash, attr.source='.numberLines',eval=FALSE, class.source="nohide"}
+container "huanjason-scikit-learn"
+```
+
+For example,
+
+```{bash, attr.source='.numberLines',eval=FALSE, class.source="nohide"}
+process {
+container "huanjason-scikit-learn"
+
+input:
+example
+
+output:
+example
+
+"""
+script section
+"""
+}
+```
+
+
+