Remove hardcoded random seeds from production config#143
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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>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Summary
--seed 1from FQ_SUBSAMPLE--runRNGseed 0from STAR_ALIGNRationale
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