Move STAR `--runRNGseed 0` out of production config into test config

[pinin4fjords]

Background

conf/modules.config pins --runRNGseed 0 on STAR in two places:

• the bare withName: 'STAR_ALIGN' block (genome alignment), and
• .*:EXTENDED_ORF_SECOND_PASS_ALIGN:FASTQ_ALIGN_STAR_HYBRID:STAR_ALIGN (hybrid second pass).

Seeds for snapshot reproducibility belong in the test config (tests/nextflow.config already does this for ribodetector/bowtie2), not in the production process config.

Why this is worth changing

• STAR already uses a fixed default RNG seed (777), so overriding it to 0 in production buys nothing for real-world reproducibility.
• It does not fix the non-determinism it appears aimed at: the hybrid second-pass alignment is non-deterministic because of thread-order-dependent multimapper assignment over the redundant canonical+novel transcriptome (verified: Log.final.out and per-transcript idxstats differ run-to-run with the seed set). That is a STAR multithreading property, not an RNG-seed one.

Proposed change

• Remove --runRNGseed 0 from conf/modules.config (both STAR blocks).
• If an explicit seed is wanted for test snapshot stability, set it in tests/nextflow.config only. Note ext.args in the test config replaces rather than appends, so this needs either re-specifying the STAR args there or a small params-based seed hook.

Note

Removing the seed re-baselines every alignment-derived snapshot (all pipeline tests use STAR), so it should be done as a focused change with a full snapshot regeneration on the CI architecture.

Context: surfaced during the determinism audit for the modernisation work (PR #174).