tluquez · tluquez · Sep 17, 2018 · Sep 17, 2018 · Sep 17, 2018 · Sep 17, 2018
diff --git a/Docs/QUARS_logo.png b/Docs/QUARS_logo.png
diff --git a/Docs/multiqc_report_paired.html → Docs/QUARS_paired.html b/Docs/multiqc_report_paired.html → Docs/QUARS_paired.html
diff --git a/Docs/multiqc_report_single.html → Docs/QUARS_single.html b/Docs/multiqc_report_single.html → Docs/QUARS_single.html
diff --git a/Docs/report_QUARS.html b/Docs/report_QUARS.html
diff --git a/Docs/timeline_QUARS.html b/Docs/timeline_QUARS.html
@@ -0,0 +1,233 @@
+<!doctype html>
+<!--
+  ~ Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
+  ~ Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
+  ~
+  ~   This file is part of 'Nextflow'.
+  ~
+  ~   Nextflow is free software: you can redistribute it and/or modify
+  ~   it under the terms of the GNU General Public License as published by
+  ~   the Free Software Foundation, either version 3 of the License, or
+  ~   (at your option) any later version.
+  ~
+  ~   Nextflow is distributed in the hope that it will be useful,
+  ~   but WITHOUT ANY WARRANTY; without even the implied warranty of
+  ~   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  ~   GNU General Public License for more details.
+  ~
+  ~   You should have received a copy of the GNU General Public License
+  ~   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+  -->
+
+<html>
+<head>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<script type="text/javascript">
+var prot = (("https:" == document.location.protocol) ? "https://" : "http://");
+document.write(unescape("%3Cscript src='" + prot + "code.jquery.com/jquery-latest.min.js' type='text/javascript' %3E%3C/script%3E"));
+document.write(unescape("%3Cscript src='" + prot + "d3js.org/d3.v3.min.js' charset='utf-8' type='text/javascript' %3E%3C/script%3E"));
+document.write(unescape("%3Cscript src='" + prot + "cdn.rawgit.com/nextflow-io/d3-timeline/82622c4cc35bac7283b3a317826b0709ac1ae476/src/d3-timeline.js' type='text/javascript' %3E%3C/script%3E"));
+</script>
+<style type="text/css">
+* {
+  font-family: 'Lato', 'Helvetica Neue', Arial, Helvetica, sans-serif;
+}
+
+.axis path,
+.axis line {
+fill: none;
+  stroke: black;
+  shape-rendering: crispEdges;
+}
+
+.axis text {
+  font-size: 10px;
+}
+
+div#timeline g text {
+  font-size: 13px;
+}
+
+text.timeline-label {
+  font-size: 13px;
+}
+
+#timeline2 .axis {
+  transform: translate(0px,30px);
+  -ms-transform: translate(0px,30px); /* IE 9 */
+  -webkit-transform: translate(0px,30px); /* Safari and Chrome */
+  -o-transform: translate(0px,30px); /* Opera */
+  -moz-transform: translate(0px,30px); /* Firefox */
+}
+
+.coloredDiv {
+  height:20px; width:20px; float:left;
+}
+
+#footer {
+  padding-top: 3em; color: #bfbfbf; font-size: 13px;
+}
+
+#footer a:visited {
+  color: #bfbfbf;
+  text-decoration: underline;
+}
+</style>
+<script type="text/javascript">
+var handler=null;
+// see https://github.com/mbostock/d3/wiki/Ordinal-Scales#category20c
+var colors = d3.scale.category20c().domain(d3.range(0,20)).range()
+
+function c0(index) { return "#9c9c9c"; }
+function c1(index) { return "#bdbdbd"; }
+function c2(index) { return colors[index % 16]; } // <-- note: uses only the first 16 colors
+
+var elapsed="1m 39s"
+var beginningMillis=1536931702316;
+var endingMillis=1536935610454;
+var data=[
+{"label": "fastp (SRR5442956)", "times": [{"starting_time": 1536932355797, "ending_time": 1536932355884, "color":c1(0)}, {"starting_time": 1536932355884, "ending_time": 1536932584351, "color":c0(0), "label": "3m 53s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932584351, "ending_time": 1536932588560, "color":c1(0)}]},
+{"label": "fastQC (SRR5442950)", "times": [{"starting_time": 1536932355538, "ending_time": 1536932355586, "color":c1(1)}, {"starting_time": 1536932355586, "ending_time": 1536932647597, "color":c0(1), "label": "4m 56s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932647597, "ending_time": 1536932651593, "color":c1(1)}]},
+{"label": "fastp (SRR5442969)", "times": [{"starting_time": 1536931702442, "ending_time": 1536931702476, "color":c1(0)}, {"starting_time": 1536931702476, "ending_time": 1536931921575, "color":c0(0), "label": "3m 44s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536931921575, "ending_time": 1536931926683, "color":c1(0)}]},
+{"label": "fastp (SRR5442949)", "times": [{"starting_time": 1536932355772, "ending_time": 1536932355796, "color":c1(0)}, {"starting_time": 1536932355796, "ending_time": 1536932595854, "color":c0(0), "label": "4m 4s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932595854, "ending_time": 1536932599456, "color":c1(0)}]},
+{"label": "fastQC (SRR5442956)", "times": [{"starting_time": 1536932355673, "ending_time": 1536932355691, "color":c1(1)}, {"starting_time": 1536932355691, "ending_time": 1536932646831, "color":c0(1), "label": "4m 53s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932646831, "ending_time": 1536932648493, "color":c1(1)}]},
+{"label": "fastQC (SRR5442954)", "times": [{"starting_time": 1536932355649, "ending_time": 1536932355689, "color":c1(1)}, {"starting_time": 1536932355689, "ending_time": 1536932637867, "color":c0(1), "label": "4m 45s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932637867, "ending_time": 1536932640956, "color":c1(1)}]},
+{"label": "fastQC (SRR5442957)", "times": [{"starting_time": 1536932355627, "ending_time": 1536932355687, "color":c1(1)}, {"starting_time": 1536932355687, "ending_time": 1536932626815, "color":c0(1), "label": "4m 34s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932626815, "ending_time": 1536932629671, "color":c1(1)}]},
+{"label": "fastQC (SRR5442955)", "times": [{"starting_time": 1536931702347, "ending_time": 1536931702378, "color":c1(1)}, {"starting_time": 1536931702378, "ending_time": 1536931978357, "color":c0(1), "label": "4m 39s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536931978357, "ending_time": 1536931981530, "color":c1(1)}]},
+{"label": "fastQC (SRR5442958)", "times": [{"starting_time": 1536932355621, "ending_time": 1536932355685, "color":c1(1)}, {"starting_time": 1536932355685, "ending_time": 1536932653511, "color":c0(1), "label": "4m 58s \/ 6.8 GB \/ CACHED"}, {"starting_time": 1536932653511, "ending_time": 1536932653700, "color":c1(1)}]},
+{"label": "fastQC (SRR5442949)", "times": [{"starting_time": 1536932355569, "ending_time": 1536932355594, "color":c1(1)}, {"starting_time": 1536932355594, "ending_time": 1536932646626, "color":c0(1), "label": "4m 53s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932646626, "ending_time": 1536932648463, "color":c1(1)}]},
+{"label": "fastQC (SRR5442959)", "times": [{"starting_time": 1536931702379, "ending_time": 1536931702466, "color":c1(1)}, {"starting_time": 1536931702466, "ending_time": 1536931978466, "color":c0(1), "label": "4m 37s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536931978466, "ending_time": 1536931979075, "color":c1(1)}]},
+{"label": "fastQC (SRR5442951)", "times": [{"starting_time": 1536932355592, "ending_time": 1536932355610, "color":c1(1)}, {"starting_time": 1536932355610, "ending_time": 1536932646536, "color":c0(1), "label": "4m 56s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932646536, "ending_time": 1536932651390, "color":c1(1)}]},
+{"label": "fastQC (SRR5442952)", "times": [{"starting_time": 1536932355681, "ending_time": 1536932355693, "color":c1(1)}, {"starting_time": 1536932355693, "ending_time": 1536932646898, "color":c0(1), "label": "4m 53s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932646898, "ending_time": 1536932648456, "color":c1(1)}]},
+{"label": "fastQC (SRR5442972)", "times": [{"starting_time": 1536931702370, "ending_time": 1536931702385, "color":c1(1)}, {"starting_time": 1536931702385, "ending_time": 1536932027227, "color":c0(1), "label": "5m 26s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932027227, "ending_time": 1536932028295, "color":c1(1)}]},
+{"label": "fastp (SRR5442960)", "times": [{"starting_time": 1536931863240, "ending_time": 1536931863973, "color":c1(0)}, {"starting_time": 1536931863973, "ending_time": 1536932020505, "color":c0(0), "label": "2m 39s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932020505, "ending_time": 1536932022715, "color":c1(0)}]},
+{"label": "fastQC (SRR5442969)", "times": [{"starting_time": 1536932355611, "ending_time": 1536932355682, "color":c1(1)}, {"starting_time": 1536932355682, "ending_time": 1536932629759, "color":c0(1), "label": "4m 35s \/ 6.8 GB \/ CACHED"}, {"starting_time": 1536932629759, "ending_time": 1536932630469, "color":c1(1)}]},
+{"label": "fastp (SRR5442958)", "times": [{"starting_time": 1536931702428, "ending_time": 1536931702471, "color":c1(0)}, {"starting_time": 1536931702471, "ending_time": 1536931912932, "color":c0(0), "label": "3m 35s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536931912932, "ending_time": 1536931917533, "color":c1(0)}]},
+{"label": "fastp (SRR5442970)", "times": [{"starting_time": 1536931702476, "ending_time": 1536931702566, "color":c1(0)}, {"starting_time": 1536931702566, "ending_time": 1536931883954, "color":c0(0), "label": "3m 2s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536931883954, "ending_time": 1536931884813, "color":c1(0)}]},
+{"label": "fastp (SRR5442951)", "times": [{"starting_time": 1536932355716, "ending_time": 1536932355791, "color":c1(0)}, {"starting_time": 1536932355791, "ending_time": 1536932591970, "color":c0(0), "label": "3m 59s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932591970, "ending_time": 1536932594266, "color":c1(0)}]},
+{"label": "fastp (SRR5442957)", "times": [{"starting_time": 1536932355728, "ending_time": 1536932355792, "color":c1(0)}, {"starting_time": 1536932355792, "ending_time": 1536932592177, "color":c0(0), "label": "3m 59s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932592177, "ending_time": 1536932594231, "color":c1(0)}]},
+{"label": "fastp (SRR5442954)", "times": [{"starting_time": 1536932355699, "ending_time": 1536932355787, "color":c1(0)}, {"starting_time": 1536932355787, "ending_time": 1536932561825, "color":c0(0), "label": "3m 30s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932561825, "ending_time": 1536932565730, "color":c1(0)}]},
+{"label": "fastp (SRR5442953)", "times": [{"starting_time": 1536932355785, "ending_time": 1536932355800, "color":c1(0)}, {"starting_time": 1536932355800, "ending_time": 1536932607071, "color":c0(0), "label": "4m 16s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932607071, "ending_time": 1536932611695, "color":c1(0)}]},
+{"label": "fastp (SRR5442955)", "times": [{"starting_time": 1536931702529, "ending_time": 1536931702571, "color":c1(0)}, {"starting_time": 1536931702571, "ending_time": 1536931860421, "color":c0(0), "label": "2m 41s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536931860421, "ending_time": 1536931863205, "color":c1(0)}]},
+{"label": "fastp (SRR5442972)", "times": [{"starting_time": 1536932355708, "ending_time": 1536932355789, "color":c1(0)}, {"starting_time": 1536932355789, "ending_time": 1536932574970, "color":c0(0), "label": "3m 41s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932574970, "ending_time": 1536932577065, "color":c1(0)}]},
+{"label": "fastp (SRR5442950)", "times": [{"starting_time": 1536932355779, "ending_time": 1536932355797, "color":c1(0)}, {"starting_time": 1536932355797, "ending_time": 1536932594636, "color":c0(0), "label": "4m 1s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932594636, "ending_time": 1536932596427, "color":c1(0)}]},
+{"label": "fastQC (SRR5442970)", "times": [{"starting_time": 1536931702316, "ending_time": 1536931702370, "color":c1(1)}, {"starting_time": 1536931702370, "ending_time": 1536931983419, "color":c0(1), "label": "4m 45s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536931983419, "ending_time": 1536931987353, "color":c1(1)}]},
+{"label": "fastQC (SRR5442971)", "times": [{"starting_time": 1536931702398, "ending_time": 1536931702468, "color":c1(1)}, {"starting_time": 1536931702468, "ending_time": 1536932020467, "color":c0(1), "label": "5m 20s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536932020467, "ending_time": 1536932022816, "color":c1(1)}]},
+{"label": "fastQC (SRR5442960)", "times": [{"starting_time": 1536931702332, "ending_time": 1536931702374, "color":c1(1)}, {"starting_time": 1536931702374, "ending_time": 1536931977484, "color":c0(1), "label": "4m 39s \/ 6.9 GB \/ CACHED"}, {"starting_time": 1536931977484, "ending_time": 1536931981675, "color":c1(1)}]},
+{"label": "fastQC (SRR5442953)", "times": [{"starting_time": 1536932355578, "ending_time": 1536932355608, "color":c1(1)}, {"starting_time": 1536932355608, "ending_time": 1536932664202, "color":c0(1), "label": "5m 9s \/ 6.8 GB \/ CACHED"}, {"starting_time": 1536932664202, "ending_time": 1536932664879, "color":c1(1)}]},
+{"label": "fastp (SRR5442952)", "times": [{"starting_time": 1536932355691, "ending_time": 1536932355783, "color":c1(0)}, {"starting_time": 1536932355783, "ending_time": 1536932595267, "color":c0(0), "label": "4m 4s \/ 1.6 GB \/ CACHED"}, {"starting_time": 1536932595267, "ending_time": 1536932599605, "color":c1(0)}]},
+{"label": "fastp (SRR5442959)", "times": [{"starting_time": 1536935513074, "ending_time": 1536935513181, "color":c1(0)}, {"starting_time": 1536935513181, "ending_time": 1536935596855, "color":c2(0), "label": "1m 26s \/ 1.6 GB"}, {"starting_time": 1536935596855, "ending_time": 1536935598993, "color":c1(0)}]},
+{"label": "multiQC", "times": [{"starting_time": 1536935599033, "ending_time": 1536935599094, "color":c1(2)}, {"starting_time": 1536935599094, "ending_time": 1536935605841, "color":c2(2), "label": "10.6s \/ 1 GB"}, {"starting_time": 1536935605841, "ending_time": 1536935609631, "color":c1(2)}]}
+]
+
+
+function getTickFormat() {
+  var MIN = 1000 * 60
+  var HOUR = MIN * 60
+  var DAY = HOUR * 24
+  var delta = (endingMillis - beginningMillis)
+
+  if( delta < 2 * MIN ) {
+    return {
+      format: d3.time.format("%S"),
+      tickTime: d3.time.seconds,
+      tickInterval: 5,
+      tickSize: 6
+    }
+  }
+
+  if( delta < 2 * HOUR ) {
+    return {
+      format: d3.time.format("%M"),
+      tickTime: d3.time.minutes,
+      tickInterval: 5,
+      tickSize: 6
+    }
+  }
+
+  if( delta < 2 * DAY ) {
+    return {
+      format: d3.time.format("%H:%M"),
+      tickTime: d3.time.hours,
+      tickInterval: 1,
+      tickSize: 6
+    }
+  }
+
+  if( delta <= 7 * DAY ) {
+    return {
+      format: d3.time.format("%b %e %H:%M"),
+      tickTime: d3.time.hours,
+      tickInterval: 6,
+      tickSize: 6
+    }
+  }
+
+  return {
+    format: d3.time.format("%b %e"),
+    tickTime: d3.time.days,
+    tickInterval: 1,
+    tickSize: 6
+  }
+}
+
+function getLabelMargin(scale) {
+    $('<span class="labelSpan" style="display: none"></span>').appendTo('body');
+
+    var labelMargin = 0
+    $.each(data, function (key, value) {
+      labelMargin = Math.max(labelMargin, $('.labelSpan').html(value.label).width());
+    });
+
+    $('.labelSpan').remove();
+
+    return (labelMargin * scale);
+}
+
+function render() {
+  handler=null;
+  $("#timeline").empty()
+  $('#label_elapsed').text(elapsed)
+  $('#label_launch').text( d3.time.format('%d %b %Y %H:%M')(new Date(beginningMillis)) )
+
+  var width = $(window).width();
+  var chart = d3.timeline()
+    .stack() // toggles graph stacking
+    .margin({left:getLabelMargin(0.85), right:100, top:0, bottom:0})
+    .tickFormat( getTickFormat() )
+    .rowSeperators('#f5f5f5')
+    .showTimeAxisTick()
+    ;
+  var svg = d3.select("#timeline").append("svg").attr("width", width).datum(data).call(chart);
+}
+
+function hrz() {
+if( handler != null ) clearTimeout(handler)
+  handler = setTimeout(render, 150);
+}
+
+$(document).ready(render)
+$(window).resize(hrz); // resize the applet on window resize
+</script>
+</head>
+
+<body>
+<div>
+  <h3>Processes execution timeline</h3>
+  <p>
+    Launch time: <span id='label_launch'> </span><br>
+    Elapsed time: <span id='label_elapsed'> </span>
+  </p>
+  <div id="timeline"></div>
+</div>
+
+<div id='footer'>
+  Created with Nextflow -- <a href='http://www.nextflow.io' target='_blank'>http://nextflow.io</a>
+</div>
+
+<script type="text/javascript">
+var prot = (("https:" == document.location.protocol) ? "https://" : "http://");
+document.write(unescape("%3Clink href='" + prot + "fonts.googleapis.com/css?family=Lato' rel='stylesheet' type='text/css' %3E%3C/link%3E"));
+</script>
+</body>
+</html>