bismark/align: intra-instance -p threading (replace --multicore fork model for Bowtie 2 + HISAT2)

[FelixKrueger]

What & why

bismark/align auto-sets --multicore N. For Bowtie 2 that forks N workers, each loading the 2 (directional/pbat) or 4 (non-directional) converted-strand indexes — so peak RAM scales with N, and the cpus/3,cpus/5 divisor leaves cores idle.

This replaces the fork model with intra-instance threading: -p = task.cpus / n_instances (n = 2 directional/pbat, 4 non-directional, 1 for --combined_index). One index load per strand, all cpus used. Applies to Bowtie 2 and HISAT2; minimap2/rammap keep the legacy --multicore path (bismark can't route -p to them yet). An explicit --multicore/-p/--parallel in ext.args still short-circuits the auto-compute.

Bowtie 2 output stays byte-identical — -p N --reorder is thread-invariant (verified 3-way against a single-core oracle). Benchmark (GRCh38, 2 M PE): wall −38 to −46 %, peak RAM −44 to −82 %.

Testing

nf-test green. The 5 existing tests are untouched — at the default cpus=2 no -p is emitted, so no snapshots regenerate; 4 new tests assert the emitted -p (from the report's options echo) at the 4-cpu CI ceiling.

Checklist

• Description of changes with reason (above)
• Tests added; nf-test passes in CI
• No version bump / modules.json change

[FelixKrueger]

Thanks @mashehu! Two notes on these:

1. Long name — good call. The catch is that the module invokes bismark (not bowtie2 directly), and bismark's CLI currently defines -p as short-only — no --threads alias, unlike bowtie2 itself — so bismark --threads N would fail to parse against the shipped 3.1.0 container. I've added a --threads alias to bismark (aligner: route -p to minimap2/rammap -t (thread-invariant, default -t 2) FelixKrueger/Bismark#1075); once a bismark release carrying it lands and this module bumps to that container, we can switch the flag here. Keeping -p for now so the module works against the current bismark:3.1.0.

2. Test assertion — I've kept -p 2 --reorder rather than --threads 2: the assertion checks the alignment report, which echoes the underlying bowtie2 command. bismark always constructs that with -p internally regardless of how threads are passed to bismark, so --threads never appears in the report — the assertion has to stay -p.