fix: add version constraint to utils/nextflow env yaml

[tedil]

As a less invasive alternative to snakemake/snakedeploy#107 this PR adds a version constraint to the nextflow version in the environment.yaml so snakedeploy update-conda-envs --pin-envs can actually pick up changes.

Summary by CodeRabbit

• Chores
  • Pinned Nextflow to version 25.04.8 for consistent, repeatable environments.
  • Refreshed Linux environment pins with updated packages and libraries to improve compatibility and stability.
  • Added metadata to the environment pin file for clearer provenance.

[coderabbitai]

📝 Walkthrough

Walkthrough

Updated Nextflow environment configuration: pinned Nextflow to version 25.04.8 in environment.yaml and regenerated the explicit linux-64 conda lock/pin file with updated package URLs, versions, and metadata.

Changes

Cohort / File(s)	Summary
Nextflow Conda pin set (linux-64) utils/nextflow/environment.linux-64.pin.txt	Replaced prior explicit pins with a new, expanded set of linux-64 packages and versions; added a created-by metadata line; numerous system/library/tooling updates and removals with updated URLs.
Environment spec version pin utils/nextflow/environment.yaml	Changed dependency to pin Nextflow exactly: from - nextflow to - nextflow =25.04.8.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description Check	⚠️ Warning	The pull request description explains the motivation and change but omits the required QC checklist and confirmation of guideline compliance defined in the repository’s PR template, leaving out the section for ticking off the contributing and testing requirements.	Please update the PR description to include the QC section from the template with the checklist items for documentation adherence, test updates, and conda environment minimal channel usage, and mark the relevant boxes to confirm guideline compliance.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title Check	✅ Passed	The title clearly summarizes the primary change by indicating a fix that adds a version constraint to the Nextflow environment YAML under utils/nextflow and follows the conventional commit “fix:” style. It is concise, directly related to the main update in the pull request, and provides sufficient context for a reviewer skimming the history.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch utils/nextflow/add-constraints

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📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 502ef25 and 5294ed7.

📒 Files selected for processing (2)

• utils/nextflow/environment.linux-64.pin.txt (1 hunks)
• utils/nextflow/environment.yaml (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)

• GitHub Check: testing
• GitHub Check: Summary

🔇 Additional comments (1)

utils/nextflow/environment.yaml (1)

6-6: Fix match spec spacing for conda.

Line 6 currently spells the dependency as nextflow =25.04.8. Conda’s dependency specs don’t permit spaces around the = operator; leaving the space causes the solver to treat the entry as a literal string and the environment creation fails. Please tighten it to nextflow=25.04.8.

-- nextflow =25.04.8
+- nextflow=25.04.8

⛔ Skipped due to learnings

Learnt from: tdayris
PR: snakemake/snakemake-wrappers#4159
File: bio/pyfaidx/environment.yaml:6-6
Timestamp: 2025-06-02T07:56:35.854Z
Learning: In the Snakemake-wrapper repository, conda dependency version pinning in environment.yaml files uses spaces around the equals sign (e.g., `- pyfaidx =0.8.1.4`) as the established coding standard, even though conda itself doesn't require the spaces.

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[tedil]

@fgvieira Any clue why the tests fail? Depending on run, we get permission errors on different binaries, e.g.,: ERROR test_wrappers.py::test_nextflow - PermissionError: [Errno 1] Operation not permitted: '/tmp/tmph3a872do/tmp8_ww334l/test/work/1a/290ea65c12de7b2287946c9c37d146/size_factors'

[fgvieira]

Not very familiar with nextflow but re-running the same test, gives a different error:
ERROR test_wrappers.py::test_nextflow - PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpalhsifqj/tmpxs93imm6/test/work/a3/f167abb4500d9e1f3ca22d09bf4427/multiqc_plots'

Maybe something to do with temp space?