Update reports

.github/workflows/integration_tests.yml

@@ -37,7 +37,7 @@ jobs:
       run: |
         mkdir ../CRISPResso2_copy
         cp -r * ../CRISPResso2_copy
-        
+
     - name: Copy C2_tests repo
       uses: actions/checkout@master
       with:

CRISPResso2/CRISPRessoReports/README.md

@@ -86,10 +86,16 @@ Also, note that the default commit message may have a summary of all commits, pl
 
 1. In the parent repo, switch to (or create) the branch on `CRISPRessoReports` that will have the changes you push.
 
-If you are creating a new branch based off of `CRISPRessoReports` master, run this:
+If you are creating a new branch based off of `CRISPRessoReports` master, run this to switch to the reports master branch:
 
 ``` shell
-git checkout -b <feature-branch>-reports reports/master
+git checkout reports/master
+```
+
+Then, run to actually create (and switch to) the branch that you will be working with:
+
+``` shell
+git checkout -b <feature-branch>-reports
 ```
 
 Or if you would like to push to an existing branch on `CRISPRessoReports`, run this:
@@ -106,14 +112,26 @@ git merge --squash -Xsubtree="CRISPResso2/CRISPRessoReports" --no-commit --allow
 
 *Note:* `<feature-branch>` is the branch of the parent repo that contains the changes inside the `CRISPRessoReports` sub-directory.
 
+3. Push to `CRISPRessoReports`.
+
+``` shell
+git push
+```
+
+4. Switch back to your branch on `CRISPResso` or `C2Web`.
+
+``` shell
+git checkout <feature-branch>
+```
+
 ### I am working on a feature that requires changing `CRISPRessoReports`, what do I do?
 
 If a feature that you are working on requires changes to CRISPRessoReports, you will need to perform a few steps to get setup.
 
 1. Create a feature branch in the parent repo, based on the parent repo master.
 
 ``` shell
-git checkout -b <feature-branch> origin/master
+git checkout -b <feature-branch>
 ```
 
 2. Create a feature branch on `CRISPRessoReports`.

CRISPResso2/CRISPRessoReports/templates/batchReport.html

@@ -45,7 +45,6 @@
 {% endblock %}
 
 {% block content %}
-
 <div class="row">
 <div class="col-sm-1"></div>
 <div class="col-sm-10">

CRISPResso2/CRISPRessoReports/templates/multiReport.html

@@ -46,7 +46,7 @@
 {% endblock %}
 
 {% block content %}
-
+<div class="row">
 <div class="col-sm-1"></div>
 <div class="col-sm-10">
 
@@ -61,7 +61,7 @@ <h5>{{report_name}}</h5>
               <div class='card-body p-0'>
                 <div class="list-group list-group-flush" style='max-height:80vh;overflow-y:auto'>
               {% for run_name in run_names %}
-	              <a href="{{report_data['crispresso_data_path']}}{{sub_html_files[run_name]}}" class="list-group-item list-group-item-action">{{run_name}}</a>
+	              <a href="{{sub_html_files[run_name]}}" class="list-group-item list-group-item-action">{{run_name}}</a>
                   {% endfor %}
                 </div>
               </div>
@@ -162,6 +162,7 @@ <h5>Summary Plots</h5>
 </div> {# column #} <!-- end column -->
 
 <div class="col-sm-1"></div>
+</div>
 {% endblock %}
 
 {% block foot %}

CRISPResso2/CRISPRessoReports/templates/pooledReport.html

@@ -44,7 +44,6 @@
 {% endblock %}
 
 {% block content %}
-
 <div class="row">
 <div class="col-sm-1"></div>
 <div class="col-sm-10">
@@ -60,8 +59,8 @@ <h5>{{report_name}}</h5>
                 <div class='card-body p-0'>
                     <div class="list-group list-group-flush">
                         {% for region_name in run_names %}
-	                  <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action">{{region_name}}</a>
-                      {% endfor %}
+	                    <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action">{{region_name}}</a>
+                        {% endfor %}
                     </div>
                 </div>
             </div>

CRISPResso2/CRISPRessoReports/templates/wgsReport.html

@@ -45,7 +45,6 @@
 {% endblock %}
 
 {% block content %}
-
 <div class="row">
 <div class="col-sm-1"></div>
 <div class="col-sm-10">
@@ -60,8 +59,8 @@ <h5>{{report_name}}</h5>
                 <div class="card-body p-0">
                     <div class="list-group list-group-flush">
                         {% for region_name in run_names %}
-                      <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action" id="{{region_name}}">{{region_name}}</a>
-                      {% endfor %}
+                        <a href="{{sub_html_files[region_name]}}" class="list-group-item list-group-item-action" id="{{region_name}}">{{region_name}}</a>
+                        {% endfor %}
                     </div>
                 </div>
             </div>