Fixed padding in report

Plant-Food-Research-Open · Dec 11, 2024 · 9c9145a · 9c9145a
1 parent 1e7ab55
commit 9c9145a
Show file tree

Hide file tree

Showing 8 changed files with 57 additions and 60 deletions.
diff --git a/bin/report_modules/parsers/synteny_parser.py b/bin/report_modules/parsers/synteny_parser.py
@@ -147,9 +147,12 @@ def parse_synteny_plotsr(folder_name="synteny_outputs"):
             "error_message": (
                 None
                 if error_comparisons == []
-                else "<b>Note:</b> Syri failed to detect structural rearrangements for following comparisons: "
+                else '<b style="color: red;">Error:</b> Syri failed to detect structural rearrangements for following comparisons: '
                 + ", ".join(
-                    [f"{target} with reference to {ref}" for (target, ref) in error_comparisons]
+                    [
+                        f"{target} with reference to {ref}"
+                        for (target, ref) in error_comparisons
+                    ]
                 )
                 + '. This may be due to known Syri limitations. See: <a href="https://github.com/schneebergerlab/syri/tree/ebd0f832e0df33398306f1b65f86801090c1ed49#current-limitations" target="_blank">GitHub/Syri/Limitations</a>'
             ),

diff --git a/bin/report_modules/templates/header.html b/bin/report_modules/templates/header.html
@@ -136,6 +136,7 @@
             width: 90%;
             min-width: 700px;
             margin: auto;
+            padding-bottom: 16px;
         }
 
         .dropdown select {

diff --git a/bin/report_modules/templates/hic/hic.html b/bin/report_modules/templates/hic/hic.html
@@ -58,7 +58,7 @@
         file.
       </li>
     </ul>
-
   </div>
+
   {% include 'hic/dropdown.html' %} {% include 'hic/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/kraken2/kraken2.html b/bin/report_modules/templates/kraken2/kraken2.html
@@ -11,12 +11,8 @@
     <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['KRAKEN2']['kraken2'] }}</b></p>
 
     <p class="section-para"><b>Note:</b></p>
-    <ul>
-      <li>
-        This report dynamically loads '*.kraken2.krona.html' files from the 'kraken2' folder under the output directory.
-        These files should also be moved when moving the report's HTML file.
-      </li>
-    </ul>
+    <p class="section-para">This report dynamically loads '*.kraken2.krona.html' files from the 'kraken2' folder under
+      the output directory. These files should also be moved when moving the report's HTML file.</p>
 
   </div>
   {% include 'kraken2/dropdown.html' %} {% include 'kraken2/report_contents.html' %}

diff --git a/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html b/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html
@@ -18,13 +18,8 @@
     </p>
 
     <p class="section-para"><b>Note:</b></p>
-    <ul>
-      <li>
-        This report dynamically loads '*.fcs.gx.krona.html' files from the 'ncbi_fcs_gx' folder under the output
-        directory. These files should also be moved when moving the report's HTML file.
-      </li>
-    </ul>
-
+    <p class="section-para">This report dynamically loads '*.fcs.gx.krona.html' files from the 'ncbi_fcs_gx' folder under the output
+      directory. These files should also be moved when moving the report's HTML file.</p>
   </div>
   {% include 'ncbi_fcs_gx/dropdown.html' %}
   {% include 'ncbi_fcs_gx/summary_contents.html' %}

diff --git a/bin/report_modules/templates/synteny_circos/synteny_circos.html b/bin/report_modules/templates/synteny_circos/synteny_circos.html
@@ -1,39 +1,42 @@
 <div id="SYNTENY_CIRCOS" class="tabcontent" style="display: none">
-    <div class="section-para-wrapper">
-        <p class="section-para">
-            Circos facilitates the identification and analysis of similarities and differences arising from comparisons
-            of genomes. The genome-wide alignments are performed with MUMMER.
-        </p>
-        <p class="section-para"><b>References:</b></p>
-        <p class="section-para">
-            Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009).
-            Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645.
-            <a href="https://doi.org/10.1101/gr.092759.109" target="_blank">10.1101/gr.092759.109</a>
-        </p>
-        <p class="section-para">
-            Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome
-            alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944.
-            <a href="https://doi.org/10.1371/journal.pcbi.1005944" target="_blank">10.1371/journal.pcbi.1005944</a>
-        </p>
-        <p class="section-para">
-            <b
-                >Versions: {{ all_stats_dicts['VERSIONS']['CIRCOS']['circos'] }} (CIRCOS), {{
-                all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b
-            >
-        </p>
-        <p class="section-para"><b>Notes:</b></p>
-        <ul>
-          <li>
-            Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
-            bundled together.
-          </li>
-          <li>
-            After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp has been filtered out.
-          </li>
-          <li>
-            The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may or may not be same as the sequence IDs in the corresponding FASTA files.
-          </li>
-        </ul>
-    </div>
-    {% include 'synteny_circos/dropdown.html' %} {% include 'synteny_circos/report_contents.html' %}
+  <div class="section-para-wrapper">
+    <p class="section-para">
+      Circos facilitates the identification and analysis of similarities and differences arising from comparisons
+      of genomes. The genome-wide alignments are performed with MUMMER.
+    </p>
+    <p class="section-para"><b>References:</b></p>
+    <p class="section-para">
+      Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009).
+      Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645.
+      <a href="https://doi.org/10.1101/gr.092759.109" target="_blank">10.1101/gr.092759.109</a>
+    </p>
+    <p class="section-para">
+      Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome
+      alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944.
+      <a href="https://doi.org/10.1371/journal.pcbi.1005944" target="_blank">10.1371/journal.pcbi.1005944</a>
+    </p>
+    <p class="section-para">
+      <b>Versions: {{ all_stats_dicts['VERSIONS']['CIRCOS']['circos'] }} (CIRCOS), {{
+        all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b>
+    </p>
+
+    <p class="section-para"><b>Notes:</b></p>
+    <ul>
+      <li>
+        Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
+        bundled together.
+      </li>
+      <li>
+        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp
+        has been filtered out.
+      </li>
+      <li>
+        The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may
+        or may not be same as the sequence IDs in the corresponding FASTA files.
+      </li>
+    </ul>
+
+  </div>
+
+  {% include 'synteny_circos/dropdown.html' %} {% include 'synteny_circos/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html b/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html
@@ -10,14 +10,16 @@
     <p class="section-para">
       <b>Version: {{ all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b>
     </p>
+
     <p class="section-para"><b>Notes:</b></p>
     <ul>
       <li>
         Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
         bundled together.
       </li>
       <li>
-        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp has
+        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp
+        has
         been filtered out.
       </li>
       <li>
@@ -26,5 +28,6 @@
       </li>
     </ul>
   </div>
+
   {% include 'synteny_dotplot/dropdown.html' %} {% include 'synteny_dotplot/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html
@@ -33,12 +33,8 @@
     </p>
 
     <p class="section-para"><b>Note:</b></p>
-    <ul>
-      <li>
-        This report dynamically loads '*.on.*.all/' folders from the 'synteny' folder under the output
-        directory. These folders should also be moved when moving the report's HTML file.
-      </li>
-    </ul>
+    <p>This report dynamically loads '*.on.*.all/' folders from the 'synteny' folder under the output directory. These
+      folders should also be moved when moving the report's HTML file.</p>
 
   </div>
   {% include 'synteny_plotsr/report_contents.html' %}
-Original file line number
+Diff line change
@@ Expand Up / @@ -58,7 +58,7 @@ @@
             file.
           </li>
         </ul>
       </div>
       {% include 'hic/dropdown.html' %} {% include 'hic/report_contents.html' %}
     </div>