Capture ABRA2 BAI outputs and stabilise snapshots

[Copilot]

Conda nf-tests failed because ABRA2’s BAI checksums differ from the shared snapshot across execution profiles. ABRA2 emits *.bai, not only *.bam.bai.

• Output contract: Match *.bai in the module and metadata so real index files are emitted.
• Snapshots: Compare BAI filenames without profile-dependent checksums; retain BAM read-content checks.

tuple val(meta), path("*.bai"), emit: bai, optional: true

[Lukecele]

Closing this PR as a duplicate of #13039, which has now been merged.

The merged PR includes the *.bai output pattern and the profile-independent snapshot handling needed for ABRA2. The final nf-test, lint, Conda, Docker, and Singularity checks passed; GPU jobs were correctly skipped because this module has no GPU-tagged tests.

Thanks to everyone who contributed to validating and stabilising the fix.