vcfcache

0.5.2 (2026-01-08) Added New -r/--requirements for vcfcache annotate to print cache requirements, validate tools, and show a fully substituted annotation command. Uses -y/--yaml if provided, otherwise the cache's params.snapshot.yaml. Local vcfcache list now reports variant counts for both blueprints and caches (via bcftools index -n). vcfcache push now verifies .vcfcache_complete with completed: true for blueprints and cache entries. Codecov patch coverage target set to 50% to prevent CI failures on small diffs. Zenodo metadata templates now include cache/blueprint alias keywords and a wiki link. Changed Renamed --show-command to --requirements and expanded output to explain cache YAMLs, required params, and tool checks. Local vcfcache list shows actual directory sizes (blueprints: blueprint/, caches: cache/) instead of a small file subset. vcfcache push now uses --metadata for Zenodo metadata, confirms upload contents, and supports blueprint-only uploads from a base dir or cache+blueprint uploads from a specific cache dir. Release process simplified and documented in RELEASE.md; scripts/release.sh is deprecated. README/WIKI streamlined and expanded with container-first quick start and a clear "start with --requirements" workflow. Zenodo metadata templates refreshed for gnomAD v4.1 cache uploads; older metadata placeholders removed. vcfcache list now prefers Zenodo record titles over alias-derived titles when available. vcfcache list --debug includes --debug in the download hints. blueprint-init --doi now defaults to VCFCACHE_DIR/blueprints when -o is not explicitly set. Fixed git_commit now falls back to VCFCACHE_GIT_COMMIT/GIT_COMMIT or unknown when running outside a git repo. Tests updated for .vcfcache_complete requirements and --requirements output. Zenodo record parsing now reads metadata instead of the deprecated blueprints field. tar_cache_subset now preserves root-level files (e.g., .vcfcache_complete) in uploaded tarballs.