Pin nf-core to 3.4.1 for training stability (#726)

* Pin nf-core to 3.4.1 for training stability

PR #683 enabled automatic installation of the latest nf-core version
by adding Python 3.13 support. While this approach ensures access to
new features, pinning to a specific version provides consistency
for training environments where reproducible behavior is important.

Related to #683

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Fix check-headings workflow to run on all PRs

The workflow was only triggered when markdown files changed, causing
it to be skipped entirely for non-markdown PRs. Since check-headings
is a required status check, this blocked PRs that didn't touch markdown.

Now the workflow runs on all PRs but conditionally skips the actual
check when no markdown files have changed.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

Author: pinin4fjords

.devcontainer/local-features/uv-tools/install.sh

@@ -3,4 +3,4 @@
 # Install python cli tools using uv
 
 uv tool install pre-commit
-uv tool install nf-core
+uv tool install nf-core==3.4.1

.github/workflows/check-headings.yml

@@ -2,10 +2,6 @@ name: Check Markdown Headings
 
 on:
   pull_request:
-    paths:
-      - "**.md"
-      # Transcripts headings correspond to main docs - may skip sections intentionally
-      - "!**/transcripts/**/*.md"
 
 jobs:
   check-headings:
@@ -24,4 +20,9 @@ jobs:
           files_ignore: "**/transcripts/**/*.md"
 
       - name: Run check_headings.py
+        if: steps.changed-files.outputs.any_changed == 'true'
         run: uv run .github/check_headings.py ${{ steps.changed-files.outputs.all_changed_files }}
+
+      - name: Skip check (no markdown files changed)
+        if: steps.changed-files.outputs.any_changed != 'true'
+        run: echo "No markdown files changed, skipping heading check"