[HOTFIX] Some symbols in meta not rendering correctly

docs/astro/convert_subworkflow.py

@@ -6,10 +6,11 @@
 from jinja2 import Environment, FileSystemLoader, select_autoescape
 
 from docs.astro.formatting import (
+    escape_mdx,
     format_choices,
     format_description,
     link,
-    sanitize_html_outside_codeblocks,
+    sanitize_outside_codeblocks,
 )
 
 
@@ -26,15 +27,13 @@ def channel_description_format(description):
     try:
         _structure = next(filter(lambda x: "Structure:" in x, _descr))
     except StopIteration:
-        return sanitize_html_outside_codeblocks(
-            " ".join(_descr), table_cell=True
-        )
+        return format_description("\n".join(_descr))
 
     _descr.remove(_structure)
-    _structure = _structure.replace('[', '`[', 1)[::-1].replace(']', ']`', 1)[::-1]
+    _structure = _structure.replace('[', '`[', 1)[::-1].replace(']', '`]', 1)[::-1]
     return "{}<br />{}".format(
         format_description('\n'.join(_descr)),
-        sanitize_html_outside_codeblocks(_structure, table_cell=True)
+        sanitize_outside_codeblocks(_structure, table_cell=True)
     )
 
 
@@ -69,7 +68,8 @@ def main():
         'link_tool': link,
         'channel_descr': channel_description_format,
         'format_choices': format_choices,
-        'format_description': format_description
+        'format_description': format_description,
+        'escape_mdx': escape_mdx
     })
 
     with open(f"{args.subworkflow_path}/meta.yml", "r") as f:

docs/astro/formatting.py

@@ -35,21 +35,23 @@ def escape_mdx(text):
 # ---------------------------------------------------------------------------
 
 #: Characters that must be escaped when rendering markdown inside HTML / MDX.
-_HTML_ESCAPE = {
+_ESCAPE = {
     "&": "&",
     "<": "&lt;",
     ">": "&gt;",
     '"': "&quot;",
     "'": "&#39;",
+    "{": "\\{",
+    "}": "\\}"
 }
 
 
-def sanitize_html_outside_codeblocks(text, table_cell=False):
+def sanitize_outside_codeblocks(text, table_cell=False):
     """Escape HTML-sensitive characters in markdown text, preserving code blocks.
 
     Scans the text character by character, tracking whether we're inside
     an inline code span (``...``) or a fenced code block (````` ... `````).
-    Only escapes ``&``, ``<``, ``>``, ``"`` and ``'`` when outside of code
+    Only escapes ``&``, ``<``, ``>``, ``"``, ``'``, ``{`` and ``}`` when outside of code
     regions.
 
     When *table_cell* is ``True`` (for content inside markdown table cells):
@@ -78,13 +80,13 @@ def sanitize_html_outside_codeblocks(text, table_cell=False):
                         content = content[first_nl + 1:]
                     content = content.rstrip("\n")
                     # Escape HTML inside <code> so it renders literally
-                    for char, entity in _HTML_ESCAPE.items():
+                    for char, entity in _ESCAPE.items():
                         content = content.replace(char, entity)
                     content = content.replace("\n", "<br />")
                     tags = ""
                     if lang:
                         tags = f'lang="{lang}"'
-                    result.append(f"<pre><code {tags}>{escape_mdx(content)}</code></pre>")
+                    result.append(f"<pre><code {tags}>{content}</code></pre>")
                 else:
                     result.append(text[i : end + 3])
                 i = end + 3
@@ -98,13 +100,13 @@ def sanitize_html_outside_codeblocks(text, table_cell=False):
                         lang = content[:first_nl]
                         content = content[first_nl + 1:]
                     content = content.rstrip("\n")
-                    for char, entity in _HTML_ESCAPE.items():
+                    for char, entity in _ESCAPE.items():
                         content = content.replace(char, entity)
                     content = content.replace("\n", "<br />")
                     tags = ""
                     if lang:
                         tags = f'lang="{lang}"'
-                    result.append(f"<pre><code {tags}>{escape_mdx(content)}</code></pre>")
+                    result.append(f"<pre><code {tags}>{content}</code></pre>")
                 else:
                     result.append(text[i:])
                 break
@@ -126,7 +128,7 @@ def sanitize_html_outside_codeblocks(text, table_cell=False):
 
         # -- Regular character: escape when outside code --------------------
         else:
-            result.append(_HTML_ESCAPE.get(text[i], text[i]))
+            result.append(_ESCAPE.get(text[i], text[i]))
             i += 1
 
     return "".join(result)
@@ -247,7 +249,7 @@ def format_description(description):
     """
     if not description:
         return ""
-    return sanitize_html_outside_codeblocks(
+    return sanitize_outside_codeblocks(
         collapse_line_returns(str(description)), table_cell=True
     )
 
@@ -259,5 +261,5 @@ def format_choices(choices):
         choices = [c.strip() for c in choices.split(",")]
 
     return "<br />".join(
-        [li(sanitize_html_outside_codeblocks(str(c))) for c in choices]
+        [li(sanitize_outside_codeblocks(str(c))) for c in choices]
     ) if choices else ""

docs/astro/templates/subworkflow.md.jinja2

@@ -31,7 +31,7 @@ head:
 
 {%- for channel in input %}
 {% for name, content in channel.items() -%}
-| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.mandatory | default(True) }} | {% if content.pattern %} `{{ content.pattern }}` {% endif %} |
+| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.mandatory | default(True) }} | {% if content.pattern %} `{{ content.pattern | escape_mdx }}` {% endif %} |
 {%- endfor %}
 {%- endfor %}
 </div>
@@ -48,7 +48,7 @@ head:
 
 {%- for channel in output %}
 {% for name, content in channel.items() -%}
-| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.mandatory | default(True) }} | {% if content.pattern %} `{{ content.pattern }}` {% endif %} |
+| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.mandatory | default(True) }} | {% if content.pattern %} `{{ content.pattern | escape_mdx }}` {% endif %} |
 {%- endfor %}
 {%- endfor %}
 </div>

modules/nf-neuro/harmonization/clinicalcombat/meta.yml

@@ -142,18 +142,21 @@ output:
           JSON files used to properly plot the harmonization results in a downstream MultiQC report.
           These files contain the regression curves and the percentiles computed before and after
           harmonization for all bundles of a given metric. The files have the following structure:
+
+          ```json
           {
-            "bundle_name_1": {
-              "metric1": {
-                "plot_1": { ... },
-                "plot_2": { ... },
+              "bundle_name_1": {
+                  "metric1": {
+                      "plot_1": { ... },
+                      "plot_2": { ... },
               },
-            "bundle_name_2": {
-              "metric1": {
-                "plot_1": { ... },
-                "plot_2": { ... },
+              "bundle_name_2": {
+                  "metric1": {
+                      "plot_1": { ... },
+                      "plot_2": { ... },
               }
           }
+          ```
         pattern: "*.json"
   versions:
     - versions.yml: