feat: aligners & variant callers#282

Draft

adthrasher wants to merge 30 commits intomainfrom

Commits on Dec 4, 2025

Commits on Dec 5, 2025

Commits on Dec 9, 2025

chore: avoid writing intermediate SAM to disk
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Merge branch 'feat/minimap2' of https://github.com/stjudecloud/workflows into feat/minimap2
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Commits on Dec 12, 2025

Commits on Dec 19, 2025

Commits on Dec 22, 2025

chore: add undocumented FAI requirement
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Commits on Dec 23, 2025

chore: add error checking to minimap2
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Commits on Jan 15, 2026

chore: cleanup reference files
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Commits on Jan 20, 2026

chore: minimum cores to 1
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