Update nextflow to 25.04.6

[ewels]

Update Nextflow version to 25.04.06 in devcontainer configurations as requested.

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Slack Thread

[cursor]

Cursor Agent can help with this pull request. Just @cursor in comments and I'll start working on changes in this branch.
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[ewels]

@cursoragent are there any remaining references to previous Nextflow versions?

[cursor]

I performed a comprehensive search for any remaining references to previous Nextflow versions across the codebase, including using grep to look for various version patterns and examining specific files like .snap files.

Based on my findings, here's the summary:

• Successfully Updated: All devcontainer configurations and documentation examples showing Nextflow output have been successfully updated to 25.04.6.
• Intentionally Left Unchanged: I found several references to older Nextflow versions that were intentionally left as they are for valid reasons:
  • Documentation Examples: Some documentation, particularly in setup guides, uses older versions (e.g., 23.10.0, 23.10.1) to demonstrate how to set specific versions for educational purposes.
  • Pipeline Configuration Requirements: Files like nextflow.config contain minimum version requirements (e.g., !>=24.04.2, !>=23.04.0, >=21.10.0), which specify compatibility rather than the version to be used.
  • Test Snapshot Files (.snap): These files contain historical test results and capture the exact Nextflow version used when tests were run (e.g., 24.10.0, 24.10.4, 23.10.1). Modifying these would invalidate the test results.

In conclusion, all appropriate references have been updated to 25.04.6. The remaining older version references are preserved for specific purposes such as educational examples, minimum compatibility requirements, and historical test snapshots. The update is complete and comprehensive.

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4 tasks completed

• Search for any remaining references to older Nextflow versions
• Check for any 24.x.x version references that might need updating
• Check for any 23.x.x version references in documentation
• Verify all version references are consistent across the codebase

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[vdauwera]

Has this been tested in practice? Are we ready to push it out ahead of the Cambridge Sessions?

[mribeirodantas]

I have two workshps this week, so let's wait a few days before merging, if possible :)

[vdauwera]

No rush!

[ewels]

Should we update to 25.10 now, since that's the latest stable?