Merge pull request #100 from Plant-Food-Research-Open/feature/fcssummary

Created summary presence/absence tables for NCBI FCS modules
Plant-Food-Research-Open · Jul 19, 2024 · c9620a3 · c9620a3
2 parents c5e9b56 + c9e791d
commit c9620a3
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -21,7 +21,6 @@ lint:
     - manifest.homePage
   multiqc_config: False
   template_strings: False
-  multiqc_config: False
 nf_core_version: 2.14.1
 repository_type: pipeline
 template:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,12 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-1. Added min. system requirements [#91](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/91)
+1. Created summary presence/absence tables for NCBI FCS modules [#88](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/88)
+2. Added min. system requirements [#91](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/91)
 
 ### `Fixed`
 
 1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95)
-2. Changed default branch name from `master` to `main` in nf-core template files
+2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
+3. Changed default branch name from `master` to `main` in nf-core template files
 
 ### `Dependencies`
 

diff --git a/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html b/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html
@@ -1,6 +1,7 @@
 <div class="dropdown">
     <div class="dropdown_content">
         <select id="selector_NCBI_FCS_ADAPTOR" onchange="showContent('NCBI_FCS_ADAPTOR')">
+          <option value="summary_NCBI_FCS_ADAPTOR">Summary</option>
             {% set str_hap = 'hap' %} {% for item in range(all_stats_dicts["NCBI_FCS_ADAPTOR"]|length) %}
             <option value="tabcontent_NCBI_FCS_ADAPTOR_{{all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['hap']}}">
                 {{ all_stats_dicts['NCBI_FCS_ADAPTOR'][item][str_hap] }} {% endfor %}

diff --git a/bin/report_modules/templates/ncbi_fcs_adaptor/ncbi_fcs_adaptor.html b/bin/report_modules/templates/ncbi_fcs_adaptor/ncbi_fcs_adaptor.html
@@ -7,5 +7,7 @@
         </p>
         <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['FCS_FCSADAPTOR']['FCS-adaptor'] }}</b></p>
     </div>
-    {% include 'ncbi_fcs_adaptor/dropdown.html' %} {% include 'ncbi_fcs_adaptor/report_contents.html' %}
+    {% include 'ncbi_fcs_adaptor/dropdown.html' %}
+    {% include 'ncbi_fcs_adaptor/summary_contents.html' %}
+    {% include 'ncbi_fcs_adaptor/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/ncbi_fcs_adaptor/report_contents.html b/bin/report_modules/templates/ncbi_fcs_adaptor/report_contents.html
@@ -1,9 +1,8 @@
-{% set vars = {'is_first': True} %} {% for item in range(all_stats_dicts["NCBI_FCS_ADAPTOR"]|length) %} {% set
-active_text = 'display: block' if vars.is_first else 'display: none' %}
+{% for item in range(all_stats_dicts["NCBI_FCS_ADAPTOR"]|length) %}
 <div
     id="tabcontent_NCBI_FCS_ADAPTOR_{{ all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['hap'] }}"
     class="tabcontent-NCBI_FCS_ADAPTOR"
-    style="{{ active_text }}"
+    style="display: none"
 >
     <div class="results-section">
         <div class="section-heading-wrapper">
@@ -12,7 +11,7 @@
     </div>
     {%if all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['did_detect_contamination'] %}
     <div class="section-para-wrapper">
-        <p class="section-para">Contamination detected. Subsequent pipeline modules are skipped.</p>
+        <p class="section-para">Contamination detected.{%if all_stats_dicts['PARAMS_DICT']['contamination_stops_pipeline'] %} Subsequent pipeline modules are skipped.{% endif %}</p>
     </div>
     <div class="table-outer">
         <div class="table-wrapper">{{ all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['report_table_html'] }}</div>
@@ -21,4 +20,4 @@
     <div class="section-para-wrapper"><p class="section-para">No contamination detected.</p></div>
     {% endif %}
 </div>
-{% if vars.update({'is_first': False}) %} {% endif %} {% endfor %}
+{% endfor %}
diff --git a/bin/report_modules/templates/ncbi_fcs_adaptor/summary_contents.html b/bin/report_modules/templates/ncbi_fcs_adaptor/summary_contents.html
@@ -0,0 +1,32 @@
+<div id="summary_NCBI_FCS_ADAPTOR" class="tabcontent-NCBI_FCS_ADAPTOR" style="display: block">
+    <div class="results-section">
+        <div class="section-heading-wrapper">
+            <div class="section-heading">Summary</div>
+        </div>
+
+        <div class="table-outer">
+            <div class="table-wrapper">
+                <table>
+                    <thead>
+                        <tr>
+                            <th width="20%" style="text-align: left">Assembly</th>
+                            <th width="80%" style="text-align: left">Contaminated?</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        {% for item in range(all_stats_dicts["NCBI_FCS_ADAPTOR"]|length) %}
+                        <tr>
+                            <td style="text-align: left; font-size: 16px">
+                                {{ all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['hap'] }}
+                            </td>
+                            <td style="text-align: left; font-size: 16px">
+                              {%if all_stats_dicts['NCBI_FCS_ADAPTOR'][item]['did_detect_contamination'] %}<b style="color: red;">Yes!</b>{% else %}No{% endif %}
+                            </td>
+                        </tr>
+                        {% endfor %}
+                    </tbody>
+                </table>
+            </div>
+        </div>
+    </div>
+</div>
diff --git a/bin/report_modules/templates/ncbi_fcs_gx/dropdown.html b/bin/report_modules/templates/ncbi_fcs_gx/dropdown.html
@@ -1,6 +1,7 @@
 <div class="dropdown">
     <div class="dropdown_content">
         <select id="selector_NCBI_FCS_GX" onchange="showContent('NCBI_FCS_GX')">
+            <option value="summary_NCBI_FCS_GX">Summary</option>
             {% set str_hap = 'hap' %} {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %}
             <option value="tabcontent_NCBI_FCS_GX_{{all_stats_dicts['NCBI_FCS_GX'][item]['hap']}}">
                 {{ all_stats_dicts['NCBI_FCS_GX'][item][str_hap] }} {% endfor %}

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
@@ -16,8 +16,8 @@
         <p class="section-para">
             <b>DB Version: {{ all_stats_dicts['NCBI_FCS_GX'][0]['report_meta_data'][1]['db']['build-date'] }}</b>
         </p>
-
-        <p></p>
     </div>
-    {% include 'ncbi_fcs_gx/dropdown.html' %} {% include 'ncbi_fcs_gx/report_contents.html' %}
+    {% include 'ncbi_fcs_gx/dropdown.html' %}
+    {% include 'ncbi_fcs_gx/summary_contents.html' %}
+    {% include 'ncbi_fcs_gx/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html b/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html
@@ -1,17 +1,16 @@
-{% set vars = {'is_first': True} %} {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %} {% set active_text =
-'display: block' if vars.is_first else 'display: none' %}
+{% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %}
 <div
     id="tabcontent_NCBI_FCS_GX_{{ all_stats_dicts['NCBI_FCS_GX'][item]['hap'] }}"
     class="tabcontent-NCBI_FCS_GX"
-    style="{{ active_text }}"
+    style="display: none"
 >
     <div class="results-section">
         <div class="section-heading-wrapper">
             <div class="section-heading">{{ all_stats_dicts['NCBI_FCS_GX'][item]['hap'] }}</div>
         </div>
         {%if all_stats_dicts['NCBI_FCS_GX'][item]['did_detect_contamination'] %}
         <div class="section-para-wrapper">
-            <p class="section-para">Contamination detected. Subsequent pipeline modules are skipped.</p>
+            <p class="section-para">Contamination detected.{%if all_stats_dicts['PARAMS_DICT']['contamination_stops_pipeline'] %} Subsequent pipeline modules are skipped.{% endif %}</p>
         </div>
         <div class="table-outer">
             <div class="table-wrapper">{{ all_stats_dicts['NCBI_FCS_GX'][item]['report_table_html'] }}</div>
@@ -46,4 +45,4 @@
         </div>
     </div>
 </div>
-{% if vars.update({'is_first': False}) %} {% endif %} {% endfor %}
+{% endfor %}
diff --git a/bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html b/bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html
@@ -0,0 +1,32 @@
+<div id="summary_NCBI_FCS_GX" class="tabcontent-NCBI_FCS_GX" style="display: block">
+    <div class="results-section">
+        <div class="section-heading-wrapper">
+            <div class="section-heading">Summary</div>
+        </div>
+
+        <div class="table-outer">
+            <div class="table-wrapper">
+                <table>
+                    <thead>
+                        <tr>
+                            <th width="20%" style="text-align: left">Assembly</th>
+                            <th width="80%" style="text-align: left">Contaminated?</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %}
+                        <tr>
+                            <td style="text-align: left; font-size: 16px">
+                                {{ all_stats_dicts['NCBI_FCS_GX'][item]['hap'] }}
+                            </td>
+                            <td style="text-align: left; font-size: 16px">
+                              {%if all_stats_dicts['NCBI_FCS_GX'][item]['did_detect_contamination'] %}<b style="color: red;">Yes!</b>{% else %}No{% endif %}
+                            </td>
+                        </tr>
+                        {% endfor %}
+                    </tbody>
+                </table>
+            </div>
+        </div>
+    </div>
+</div>