Expose additional parameters and document omissions (#168)

[PriyankaaXD]

Closes #168 (partially — STAR and Kraken2 specifically; other tools mentioned in the issue can be follow-ups).

Summary

Audited STAR and Kraken2 (the two tools called out in #168) for undocumented/unexposed parameters, and introduced the omitted_parameters meta key convention discussed in the issue for documenting intentional omissions in a structured, greppable way.

Changes

tools/kraken2.wdl (kraken task)

• Exposes --confidence, --minimum-hit-groups, and --quick as new inputs (confidence, minimum_hit_groups, quick)
• These were previously unexposed with no documented reason — confirmed with @a-frantz these should be exposed
• --memory-mapping was considered and intentionally not added, per discussion on the issue (unclear RAM/time tradeoff, and WDL execution environments are rarely memory-constrained)

tools/star.wdl (alignment task)

• Adds omitted_parameters documenting two previously-unexplained hardcoded flags:
  • --outSAMtype: intentionally fixed to BAM Unsorted — STAR's own sort implementation is inefficient in the worst case; sorting is handled by a dedicated downstream task instead
  • --outMultimapperOrder: intentionally fixed to Random — the alternative (Old_2.4) is a biased quasi-random order predating STAR 2.5.0 and expected to be deprecated
• No behavior change; docs-only

tools/qualimap.wdl (rnaseq task)

• Converts the existing prose explanation of the omitted -p parameter into the new omitted_parameters structure, as a reference implementation of the convention
• No behavior change; docs-only

Testing

• sprocket check passes on all three files
• sprocket dev test tools/star.wdl -t alignment: 4/4 passing
• sprocket dev test tools/kraken2.wdl -t kraken: 16/16 passing
• No new tests added: kraken2::kraken changes are covered by its existing works test above. qualimap::rnaseq has no existing test suite to extend, and this change is meta-only (no behavior change), so no new tests were needed there either.

Open questions for reviewers

• Is the omitted_parameters shape (array of {flag, reason} objects) the right convention going forward, or would you prefer something else (e.g. keyed by flag name)? Happy to adjust and propagate to other tools with known ghost omissions (STAR/Kraken2 were just the two named in the issue).

Before submitting this PR, please make sure:

• You have added a few sentences describing the PR here.
• The code passes all CI tests without any errors or warnings.
• You have added tests (when appropriate).
• You have added an entry in any relevant CHANGELOGs (when appropriate).
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• You have updated the README or other documentation to account for these changes (when appropriate).

[stjudecloud-cloudy]

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[PriyankaaXD]

Will follow up with a tools/CHANGELOG.md entry in a moment now that I have the PR number — wanted to get this open first since I needed the number to link it correctly.

[PriyankaaXD]

Added the tools/CHANGELOG.md entry — this should be ready for review now.