End of pride month, fix a handful of broken snippets

.github/workflows/ci.yml

@@ -71,6 +71,10 @@ jobs:
             --enforce-https=false \
             ./_site
 
+      - name: Ensure no unexpected encoded HTML in output
+        run: |
+          ! fgrep -R 'lt;blockquote' _site
+
       - name: Run aXe accessibility testing on some representative URLs
         run: |
           node_modules/.bin/http-server _site/ &

_config.yml

@@ -244,16 +244,16 @@ plugins:
   - jekyll-redirect-from
 
 # An announcement to display on the home page
-announcement:
-   class: success
-   title: GTN Celebrates Pride Month
-   text: |
-     June is pride month in many countries around the world! The GTN is celebrating it by remembering the story of Alan L. Hart, a trans doctor who pioneered the use of x-ray photography in tuberculosis detection.
-
-     [Read about Alan L. Hart's contribution to M. Tuberculosis](/training-material/news/2023/06/01/hart.html){: .btn.btn-primary}
-     <a href="#" class="btn btn-success" onclick="setTheme('progress')">Activate the GTN Theme!</a>
-
-     <strong>Note:</strong> You can change your theme any time via the 'Extras' menu at the top!
+#announcement:
+#   class: success
+#   title: GTN Celebrates Pride Month
+#   text: |
+#     June is pride month in many countries around the world! The GTN is celebrating it by remembering the story of Alan L. Hart, a trans doctor who pioneered the use of x-ray photography in tuberculosis detection.
+#
+#     [Read about Alan L. Hart's contribution to M. Tuberculosis](/training-material/news/2023/06/01/hart.html){: .btn.btn-primary}
+#     <a href="#" class="btn btn-success" onclick="setTheme('progress')">Activate the GTN Theme!</a>
+#
+#     <strong>Note:</strong> You can change your theme any time via the 'Extras' menu at the top!
 
 # A banner image that can be displayed separately for short wide banner images. Alt text is mandatory.
 # banner_image:

topics/assembly/tutorials/largegenome/tutorial.md

@@ -147,7 +147,9 @@ We are also using a reference genome *Arabidopsis thaliana* for a later comparis
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >    
 > 3. Check that the datatypes for the three files of sequencing reads are `fastq.gz`, not `fastqsanger.gz` and change datatype if needed.
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %}
+>
 {: .hands_on}
 
 * This tutorial uses these input files and gives some examples from the results.

topics/epigenetics/tutorials/atac-seq/tutorial.md

@@ -438,8 +438,11 @@ Because of the PCR amplification, there might be read duplicates (different read
 >    - {% icon param-file %} *"Select lines from"*: Select the output of  **MarkDuplicates** {% icon tool %}
 >    - *"that*: `Matching`
 >    - *"the pattern*: `(Library|LIBRARY)`
+>
 > 2. Check that the datatype is tabular. If not, change it.
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="tabular" %}
+>
 > 3. {% tool  [Transpose rows/columns in a tabular file](toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0) %}:
 >    - {% icon param-file %} *"Select lines from"*: Select the output of **Select** {% icon tool %}
 >

topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.md

@@ -326,46 +326,46 @@ The spectral data comes as an `.msp` file, which is a text file structured accor
 
 > <hands-on-title> Data Exploration </hands-on-title>
 >
->    Click *"View data"* {% icon galaxy-eye %} icon next to the dataset in the Galaxy history. The contents of the file would look like this:
->
->    {% snippet faqs/galaxy/datasets_icons.md %}
->
->    ```
->     NAME:C001
->     IONMODE:Negative
->     SPECTRUMTYPE:Centroid
->     RETENTIONTIME:383.27
->     Num Peaks:231
->     217.1073 64041926
->     243.0865 35597866
->     257.1134 31831229
->     224.061 27258239
->     258.11 24996353
->     241.0821 23957171
->     315.1188 13756744
->     ...
->
->     NAME:C002
->     IONMODE:Negative
->     SPECTRUMTYPE:Centroid
->     RETENTIONTIME:281.62
->     Num Peaks:165
->     307.1573 299174880
->     147.0654 298860831
->     149.0447 287809889
->     218.1066 118274758
->     189.076 112486871
->     364.1787 75134143
->     191.0916 52526567
->     308.1579 52057158
->     ...
->    ```
->
->    > <details-title> Negative ion mode </details-title>
->    >
->    > You might wonder how can the ionisation mode (_IONMODE_) for GC-MS data be negative when using electron impact (EI+) ionization. This is, of course, incorrect. This is actually just a default behaviour of **RAMClustR**. We can optionally change this by providing **RAMClustR** an experiment definition file. This file can be created manually or using the {% tool [RAMClustR define experiment](toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2) %} tool. There we can specify annotations such as what instrument we used or ionisation mode (which was EI+ in our case), and this will be transfered to the `.msp` file. Finally, we can provide such a file as an input to **RAMClustR** in the _Extras_ inputs section.
->    >
->    {: .details}
+> Click *"View data"* {% icon galaxy-eye %} icon next to the dataset in the Galaxy history. The contents of the file would look like this:
+>
+> {% snippet faqs/galaxy/datasets_icons.md %}
+>
+> ```
+> NAME:C001
+> IONMODE:Negative
+> SPECTRUMTYPE:Centroid
+> RETENTIONTIME:383.27
+> Num Peaks:231
+> 217.1073 64041926
+> 243.0865 35597866
+> 257.1134 31831229
+> 224.061 27258239
+> 258.11 24996353
+> 241.0821 23957171
+> 315.1188 13756744
+> ...
+>
+> NAME:C002
+> IONMODE:Negative
+> SPECTRUMTYPE:Centroid
+> RETENTIONTIME:281.62
+> Num Peaks:165
+> 307.1573 299174880
+> 147.0654 298860831
+> 149.0447 287809889
+> 218.1066 118274758
+> 189.076 112486871
+> 364.1787 75134143
+> 191.0916 52526567
+> 308.1579 52057158
+> ...
+> ```
+>
+> > <details-title> Negative ion mode </details-title>
+> >
+> > You might wonder how can the ionisation mode (_IONMODE_) for GC-MS data be negative when using electron impact (EI+) ionization. This is, of course, incorrect. This is actually just a default behaviour of **RAMClustR**. We can optionally change this by providing **RAMClustR** an experiment definition file. This file can be created manually or using the {% tool [RAMClustR define experiment](toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2) %} tool. There we can specify annotations such as what instrument we used or ionisation mode (which was EI+ in our case), and this will be transfered to the `.msp` file. Finally, we can provide such a file as an input to **RAMClustR** in the _Extras_ inputs section.
+> >
+> {: .details}
 >
 {: .hands_on}
 

topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.md

@@ -68,7 +68,7 @@ The "Data Upload" process is the only one in this tutorial that takes place dire
 
 > <hands-on-title>Data upload</hands-on-title>
 >
->    Import the FASTQ file pairs from [Zenodo]({{ page.zenodo_link }}) or a data library:
+> 1. Import the FASTQ file pairs from [Zenodo]({{ page.zenodo_link }}) or a data library:
 >    - `GSM461177` (untreated): `GSM461177_1` and `GSM461177_2`
 >    - `GSM461180` (treated): `GSM461180_1` and `GSM461180_2`
 >
@@ -79,9 +79,9 @@ The "Data Upload" process is the only one in this tutorial that takes place dire
 >    {{ page.zenodo_link }}/files/GSM461180_2.fastqsanger
 >    ```
 >
->    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+> 2. {% snippet faqs/galaxy/datasets_import_via_link.md %}
 >
->    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
+> 3. {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >    > <comment-title></comment-title>
 >    >
@@ -98,12 +98,11 @@ The "Data Upload" process is the only one in this tutorial that takes place dire
 >    >
 >    {: .comment}
 >
->    Change the datatype from `fastqsanger` to `fastq`.
+> 4. Change the datatype from `fastqsanger` to `fastq`.
 >
 >    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="fastq" %}
 >
->
->    We also need to import two more files, essential for the alignment operation (and basically every alignment procedure): the organism's reference genome (here *D. melanogaster*) and the organism's gene annotation.
+> 5. We also need to import two more files, essential for the alignment operation (and basically every alignment procedure): the organism's reference genome (here *D. melanogaster*) and the organism's gene annotation.
 >    Those can be aquired directly via link and Galaxy's data library as described above. For this tutorial we are going to use the files [dm6.fa.gz](https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz) and [Drosophila_melanogaster.BDGP6.87.gtf (dm6)](https://usegalaxy.eu/libraries/folders/F30cab321d898d2fb/dataset/02c5f7fcdb6bf41f). Note that it is essential to convert genome's file from `*.fa.gz` to `*.fa`. That is easy now that we have already used the same method to convert `fastqsanger` to `fastq`. Remember to change the name of the file, too, in your working history as Galaxy will not do it automatically. Doing so will prevent any confusions later on.
 >
 > {% snippet faqs/galaxy/datasets_rename.md name="dm6.fa" %}