fix: revert GTF from sc, harden Dockerfile, fix docs#92
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Jaureguy760 merged 1 commit intodevfrom Mar 15, 2026
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- Revert GTF/GFF3 support from count-variants-sc (sc commands are scATAC-only; gene annotation is a downstream ArchR/Signac step) - Bulk count-variants retains full GTF support - Dockerfile: tini PID 1, g++ purge assertion, wasp2-ipscore check - Smoke test: add wasp2-ipscore, fix sample name case - Docs: rewrite counting/mapping/analysis/installation pages - Remove stale --min-count footnote from analysis.rst Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
count-variants-sc— sc commands are scATAC-only; gene annotation is a downstream ArchR/Signac step. Bulkcount-variantsretains full GTF support.SAMPLE1→sample1)--min-countfootnote from analysis.rstTest plan
count-variants-sc --helpshows BED/Peak only, no GTF paramscount-variants --helpstill shows GTF/GFF3 options🤖 Generated with Claude Code