fix email address and add stylesheet for report

bin/computeRatio

@@ -160,7 +160,7 @@ if __name__ == "__main__":
         fw.write(
             '<img src="https://raw.githubusercontent.com/maxibor/coproID/master/img/logo.png" height="150">\n\n  ')
         fw.write(
-            '**Homepage/Documentation**: [github.com/maxibor/coproID](https://github.com/maxibor/coproID)  \n**Author:** Maxime Borry [borry@shh.mpg.de](borry@shh.mpg.de)\n\n  ')
+            '**Homepage/Documentation**: [github.com/maxibor/coproID](https://github.com/maxibor/coproID)  \n**Author:** Maxime Borry [borry@shh.mpg.de](mailto:borry@shh.mpg.de)\n\n  ')
         fw.write("Report automatically generated by coproID on " + str(now.year) + "-" + str(now.month) + "-" +
                  str(now.day) + "  " + str(now.hour) + ":" + str(now.minute) + ":" + str(now.second) + "  \n")
         fw.write("\n\n")

main.nf

@@ -78,6 +78,7 @@ params.name1 = ''
 params.name2 = ''
 params.identity = 0.85
 params.bowtie = 'very-sensitive'
+css = baseDir+'/misc/pandoc.css'
 
 bowtie_setting = ''
 
@@ -446,6 +447,6 @@ process md2html {
     script:
         outfile = name+".html"
         """
-        pandoc --self-contained --webtex -s $report -o $outfile
+        pandoc --self-contained --css $css --webtex -s $report -o $outfile
         """
 }

misc/pandoc.css

@@ -0,0 +1,328 @@
+/*
+ * I add this to html files generated with pandoc.
+ */
+
+html {
+  font-size: 100%;
+  overflow-y: scroll;
+  -webkit-text-size-adjust: 100%;
+  -ms-text-size-adjust: 100%;
+}
+
+body {
+  color: #444;
+  font-family: Georgia, Palatino, 'Palatino Linotype', Times, 'Times New Roman', serif;
+  font-size: 12px;
+  line-height: 1.7;
+  padding: 1em;
+  margin: auto;
+  max-width: 42em;
+  background: #fefefe;
+}
+
+a {
+  color: #0645ad;
+  text-decoration: none;
+}
+
+a:visited {
+  color: #0b0080;
+}
+
+a:hover {
+  color: #06e;
+}
+
+a:active {
+  color: #faa700;
+}
+
+a:focus {
+  outline: thin dotted;
+}
+
+*::-moz-selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #000;
+}
+
+*::selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #000;
+}
+
+a::-moz-selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #0645ad;
+}
+
+a::selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #0645ad;
+}
+
+p {
+  margin: 1em 0;
+}
+
+img {
+  max-width: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+  color: #111;
+  line-height: 125%;
+  margin-top: 2em;
+  font-weight: normal;
+}
+
+h4, h5, h6 {
+  font-weight: bold;
+}
+
+h1 {
+  font-size: 2.5em;
+}
+
+h2 {
+  font-size: 2em;
+}
+
+h3 {
+  font-size: 1.5em;
+}
+
+h4 {
+  font-size: 1.2em;
+}
+
+h5 {
+  font-size: 1em;
+}
+
+h6 {
+  font-size: 0.9em;
+}
+
+blockquote {
+  color: #666666;
+  margin: 0;
+  padding-left: 3em;
+  border-left: 0.5em #EEE solid;
+}
+
+hr {
+  display: block;
+  height: 2px;
+  border: 0;
+  border-top: 1px solid #aaa;
+  border-bottom: 1px solid #eee;
+  margin: 1em 0;
+  padding: 0;
+}
+
+pre, code, kbd, samp {
+  color: #000;
+  font-family: monospace, monospace;
+  _font-family: 'courier new', monospace;
+  font-size: 0.98em;
+}
+
+pre {
+  white-space: pre;
+  white-space: pre-wrap;
+  word-wrap: break-word;
+}
+
+b, strong {
+  font-weight: bold;
+}
+
+dfn {
+  font-style: italic;
+}
+
+ins {
+  background: #ff9;
+  color: #000;
+  text-decoration: none;
+}
+
+mark {
+  background: #ff0;
+  color: #000;
+  font-style: italic;
+  font-weight: bold;
+}
+
+sub, sup {
+  font-size: 75%;
+  line-height: 0;
+  position: relative;
+  vertical-align: baseline;
+}
+
+sup {
+  top: -0.5em;
+}
+
+sub {
+  bottom: -0.25em;
+}
+
+ul, ol {
+  margin: 1em 0;
+  padding: 0 0 0 2em;
+}
+
+li p:last-child {
+  margin-bottom: 0;
+}
+
+ul ul, ol ol {
+  margin: .3em 0;
+}
+
+dl {
+  margin-bottom: 1em;
+}
+
+dt {
+  font-weight: bold;
+  margin-bottom: .8em;
+}
+
+dd {
+  margin: 0 0 .8em 2em;
+}
+
+dd:last-child {
+  margin-bottom: 0;
+}
+
+img {
+  border: 0;
+  -ms-interpolation-mode: bicubic;
+  vertical-align: middle;
+}
+
+figure {
+  display: block;
+  text-align: center;
+  margin: 1em 0;
+}
+
+figure img {
+  border: none;
+  margin: 0 auto;
+}
+
+figcaption {
+  font-size: 0.8em;
+  font-style: italic;
+  margin: 0 0 .8em;
+}
+
+table {
+  margin-bottom: 2em;
+  border-bottom: 1px solid #ddd;
+  border-right: 1px solid #ddd;
+  border-spacing: 0;
+  border-collapse: collapse;
+}
+
+table th {
+  padding: .2em 1em;
+  background-color: #eee;
+  border-top: 1px solid #ddd;
+  border-left: 1px solid #ddd;
+}
+
+table td {
+  padding: .2em 1em;
+  border-top: 1px solid #ddd;
+  border-left: 1px solid #ddd;
+  vertical-align: top;
+}
+
+.author {
+  font-size: 1.2em;
+  text-align: center;
+}
+
+@media only screen and (min-width: 480px) {
+  body {
+    font-size: 14px;
+  }
+}
+@media only screen and (min-width: 768px) {
+  body {
+    font-size: 16px;
+  }
+}
+@media print {
+  * {
+    background: transparent !important;
+    color: black !important;
+    filter: none !important;
+    -ms-filter: none !important;
+  }
+
+  body {
+    font-size: 12pt;
+    max-width: 100%;
+  }
+
+  a, a:visited {
+    text-decoration: underline;
+  }
+
+  hr {
+    height: 1px;
+    border: 0;
+    border-bottom: 1px solid black;
+  }
+
+  a[href]:after {
+    content: " (" attr(href) ")";
+  }
+
+  abbr[title]:after {
+    content: " (" attr(title) ")";
+  }
+
+  .ir a:after, a[href^="javascript:"]:after, a[href^="#"]:after {
+    content: "";
+  }
+
+  pre, blockquote {
+    border: 1px solid #999;
+    padding-right: 1em;
+    page-break-inside: avoid;
+  }
+
+  tr, img {
+    page-break-inside: avoid;
+  }
+
+  img {
+    max-width: 100% !important;
+  }
+
+  @page :left {
+    margin: 15mm 20mm 15mm 10mm;
+}
+
+  @page :right {
+    margin: 15mm 10mm 15mm 20mm;
+}
+
+  p, h2, h3 {
+    orphans: 3;
+    widows: 3;
+  }
+
+  h2, h3 {
+    page-break-after: avoid;
+  }
+}