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Author: Quarto GHA Workflow Runner

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@@ -1 +1 @@
-5db0cb8c
+a19f6be8

people.html

@@ -424,7 +424,7 @@ <h1 class="title">People</h1>
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-listing-file-modified-sort="1748416382816" data-listing-reading-time-sort="1" data-listing-word-count-sort="53">
+<div class="quarto-post image-right" data-index="0" data-listing-file-modified-sort="1748421315968" data-listing-reading-time-sort="1" data-listing-word-count-sort="53">
 <div class="thumbnail"><a href="./cards/SamueleSoraggi.html" class="no-external">
 
 <p class="card-img-top"><img src="cards/samuele.jpg"  class="thumbnail-image card-img"/></p>

resources/Slides/Advanced/slides.html

@@ -1378,15 +1378,15 @@ <h2>Exercise III: Your own target!</h2>
 <li>do not make tiny and numerous jobs, try to put together things with similar resource usage</li>
 <li>start testing one of many parallel elements of a worlflow
 <ul>
-<li>determine resource usage (<code>gwf utilization</code> - needs a plugin, see exercises after)</li>
-<li>then adjust all elements accordingly</li>
+<li>determine resource usage (<code>gwf utilization</code> - needs a plugin, see earlier exercises)</li>
+<li>adjust your templates’ resources accordingly</li>
 </ul></li>
 <li>verify often your code is correct
 <ul>
-<li><code>gwf info | less -S</code> to check dependencies</li>
+<li><code>gwf info target_name</code> to check dependencies</li>
 <li>remember you are using python, check some of your code directly in it!</li>
 </ul></li>
-<li>when done, you are reproducible if you share with your datasets:ave
+<li>when done, you are reproducible if you share with your datasets:
 <ul>
 <li>container pull commands</li>
 <li>conda environment(s) package list</li>

resources/Slides/Introduction/slides.backup.html

@@ -454,10 +454,10 @@ <h2>Exercise:</h2>
 <div class="column" style="width:40%;">
 <p><img data-src="img/complexTree.png" width="300"></p>
 </div><div class="column" style="width:60%;">
-<div id="32c157e3" class="cell" data-execution_count="1">
+<div id="26dec929" class="cell" data-execution_count="1">
 <div class="cell-output cell-output-display">
-<div id="XvJVxssaXakh" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: left"><style>
-#XvJVxssaXakh {
+<div id="KQExpkRboLox" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: left"><style>
+#KQExpkRboLox {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -678,7 +678,7 @@ <h2>Exercise:</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsXvJVxssaXakh=[
+var questionsKQExpkRboLox=[
     {
         "question": "Two of the following are correct:",
         "type": "many_choice",
@@ -1794,8 +1794,8 @@ <h2>Exercise:</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("XvJVxssaXakh")) {
-    show_questions(questionsXvJVxssaXakh, XvJVxssaXakh);
+  if (document.getElementById("KQExpkRboLox")) {
+    show_questions(questionsKQExpkRboLox, KQExpkRboLox);
   } else {
     setTimeout(try_show, 200);
   }
@@ -1897,10 +1897,10 @@ <h2>Exercise: Read files</h2>
 </div>
 <div class="callout-content">
 <p>Search online (or with <code>less --help)</code> how to look for a specific word in a file with <code>less</code>. Then visualize the data with <code>less</code>, and try to find if there is any sequence of ten adjacent <code>N</code>s (which is, ten missing nucleotides). Then, answer the question below</p>
-<div id="e09d022c" class="cell" data-execution_count="2">
+<div id="09208760" class="cell" data-execution_count="2">
 <div class="cell-output cell-output-display">
-<div id="MScMkuhfeNUD" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
-#MScMkuhfeNUD {
+<div id="lCkwaWAuyDtK" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
+#lCkwaWAuyDtK {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -2121,7 +2121,7 @@ <h2>Exercise: Read files</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsMScMkuhfeNUD=[
+var questionslCkwaWAuyDtK=[
     {
         "question": "How long is the shortest sequence of missing nucleotides not found anywhere in the file data.fastq?",
         "type": "many_choice",
@@ -3211,8 +3211,8 @@ <h2>Exercise: Read files</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("MScMkuhfeNUD")) {
-    show_questions(questionsMScMkuhfeNUD, MScMkuhfeNUD);
+  if (document.getElementById("lCkwaWAuyDtK")) {
+    show_questions(questionslCkwaWAuyDtK, lCkwaWAuyDtK);
   } else {
     setTimeout(try_show, 200);
   }
@@ -3618,10 +3618,10 @@ <h2>Less for reading files</h2>
 </div>
 <div class="callout-content">
 <p>Search online (or with <code>less --help)</code> how to look for a specific word in a file with <code>less</code>. Then visualize the data with <code>less</code>, and try to find if there is any sequence of ten adjacent <code>N</code>s (which is, ten missing nucleotides). Then, answer the question below</p>
-<div id="ece008da" class="cell" data-execution_count="3">
+<div id="a2af8b5e" class="cell" data-execution_count="3">
 <div class="cell-output cell-output-display">
-<div id="gWKrDNwXmztf" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
-#gWKrDNwXmztf {
+<div id="VNoVJfjLDQsB" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
+#VNoVJfjLDQsB {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -3842,7 +3842,7 @@ <h2>Less for reading files</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsgWKrDNwXmztf=[
+var questionsVNoVJfjLDQsB=[
     {
         "question": "How long is the shortest sequence of missing nucleotides not found anywhere in the file data.fastq?",
         "type": "many_choice",
@@ -4932,8 +4932,8 @@ <h2>Less for reading files</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("gWKrDNwXmztf")) {
-    show_questions(questionsgWKrDNwXmztf, gWKrDNwXmztf);
+  if (document.getElementById("VNoVJfjLDQsB")) {
+    show_questions(questionsVNoVJfjLDQsB, VNoVJfjLDQsB);
   } else {
     setTimeout(try_show, 200);
   }
@@ -5046,10 +5046,10 @@ <h2>Piping</h2>
 <p>The output of that pipe was a small output on screen - but <strong>outputs can be huge</strong>! We could count the number of sequences by piping again into <code>wc</code>!</p>
 <div class="sourceCode" id="cb48"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb48-1"><a aria-hidden="true" tabindex="-1"></a><span class="fu">head</span> <span class="at">-400</span> dataOriginal.fastq <span class="kw">|</span> <span class="fu">grep</span> NNNNN <span class="kw">|</span> <span class="fu">wc</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>&nbsp;</p>
-<div id="83e87c6b" class="cell" data-execution_count="4">
+<div id="68327f93" class="cell" data-execution_count="4">
 <div class="cell-output cell-output-display">
-<div id="OnwKBzXloUiY" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
-#OnwKBzXloUiY {
+<div id="uUnjDOgYxrVa" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
+#uUnjDOgYxrVa {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -5270,7 +5270,7 @@ <h2>Piping</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsOnwKBzXloUiY=[
+var questionsuUnjDOgYxrVa=[
     {
         "question": "Wait a second! That sequence absolutely needs to be saved into a file. How do you do it?",
         "type": "many_choice",
@@ -6360,8 +6360,8 @@ <h2>Piping</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("OnwKBzXloUiY")) {
-    show_questions(questionsOnwKBzXloUiY, OnwKBzXloUiY);
+  if (document.getElementById("uUnjDOgYxrVa")) {
+    show_questions(questionsuUnjDOgYxrVa, uUnjDOgYxrVa);
   } else {
     setTimeout(try_show, 200);
   }

resources/Slides/Introduction/slides.html

@@ -454,10 +454,10 @@ <h2>Exercise:</h2>
 <div class="column" style="width:40%;">
 <p><img data-src="img/complexTree.png" width="300"></p>
 </div><div class="column" style="width:60%;">
-<div id="2f0f4d7b" class="cell" data-execution_count="1">
+<div id="9a67fd88" class="cell" data-execution_count="1">
 <div class="cell-output cell-output-display">
-<div id="OAsJxGBzgrVc" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: left"><style>
-#OAsJxGBzgrVc {
+<div id="pxlUfHDPuxRu" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: left"><style>
+#pxlUfHDPuxRu {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -678,7 +678,7 @@ <h2>Exercise:</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsOAsJxGBzgrVc=[
+var questionspxlUfHDPuxRu=[
     {
         "question": "Two of the following are correct:",
         "type": "many_choice",
@@ -1794,8 +1794,8 @@ <h2>Exercise:</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("OAsJxGBzgrVc")) {
-    show_questions(questionsOAsJxGBzgrVc, OAsJxGBzgrVc);
+  if (document.getElementById("pxlUfHDPuxRu")) {
+    show_questions(questionspxlUfHDPuxRu, pxlUfHDPuxRu);
   } else {
     setTimeout(try_show, 200);
   }
@@ -1896,10 +1896,10 @@ <h2>Exercise: Read files</h2>
 </div>
 <div class="callout-content">
 <p>Search online (or with <code>less --help)</code> how to look for a specific word in a file with <code>less</code>. Then visualize the data with <code>less</code>, and try to find if there is any sequence of ten adjacent <code>N</code>s (which is, ten missing nucleotides). Then, answer the question below</p>
-<div id="cc317e18" class="cell" data-execution_count="2">
+<div id="6ae6c8b5" class="cell" data-execution_count="2">
 <div class="cell-output cell-output-display">
-<div id="EBbvhqJyHaBd" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
-#EBbvhqJyHaBd {
+<div id="yRMWDJXBlNKN" data-shufflequestions="False" data-shuffleanswers="True" data-preserveresponses="false" data-numquestions="1000000" data-maxwidth="600" style="border-radius: 10px; text-align: center"><style>
+#yRMWDJXBlNKN {
    --jq-multiple-choice-bg: #6f78ffff;
    --jq-mc-button-bg: #fafafa;
    --jq-mc-button-border: #e0e0e0e0;
@@ -2120,7 +2120,7 @@ <h2>Exercise: Read files</h2>
 </div>
 <div class="cell-output cell-output-display">
 <script type="application/javascript">
-var questionsEBbvhqJyHaBd=[
+var questionsyRMWDJXBlNKN=[
     {
         "question": "How long is the shortest sequence of missing nucleotides not found anywhere in the file data.fastq?",
         "type": "many_choice",
@@ -3210,8 +3210,8 @@ <h2>Exercise: Read files</h2>
  * Ensures show_questions is called after the container div is in the DOM.
  */
 function try_show() {
-  if (document.getElementById("EBbvhqJyHaBd")) {
-    show_questions(questionsEBbvhqJyHaBd, EBbvhqJyHaBd);
+  if (document.getElementById("yRMWDJXBlNKN")) {
+    show_questions(questionsyRMWDJXBlNKN, yRMWDJXBlNKN);
   } else {
     setTimeout(try_show, 200);
   }