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Remove hardcoded random seeds from production config #143

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Remove hardcoded random seeds from production config #143

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@pinin4fjords pinin4fjords commented Jan 19, 2026

Summary

  • Remove --seed 1 from FQ_SUBSAMPLE
  • Remove --runRNGseed 0 from STAR_ALIGN

Rationale

Fixed seeds create an illusion of reproducibility but results can still vary across CPU architectures, thread scheduling, and container rebuilds, so "same seed ≠ same results" in practice. If changing the seed meaningfully changes the outcome, that result is inherently unreliable and fixing the seed just hides the problem rather than addressing it.

Seeds remain in test configs where they are appropriate for snapshot stability.

Note

The nf-core umitools/dedup module also has a hardcoded seed (--random-seed=100) but that would need an upstream fix.

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits January 19, 2026 09:40
@pinin4fjords @claude
Remove hardcoded random seeds from production config
aab7404 
Remove fixed seeds from FQ_SUBSAMPLE and STAR_ALIGN. Fixed seeds create
an illusion of reproducibility but results can still vary across CPU
architectures, thread scheduling, and container rebuilds. If changing
the seed meaningfully changes the outcome, that result is inherently
unreliable and fixing the seed just hides the problem.

Seeds remain in test configs where they are appropriate for snapshot
stability.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update CHANGELOG with PR #143
9c2b9a5 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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github-actions bot commented Jan 19, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c2b9a5

+| ✅ 269 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/riboseq/riboseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: assets/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-19 09:46:05

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