Test data e2e-data-1

Copies of the pinned public data the e2e cases read, so a CI leg with no Actions cache does not wait on EBI: the 1000 Genomes phase 3 v5c sites VCF (md5 in versions.env, ARCHAIC_1KG_SITES_MD5). scripts/ci/e2e-run.sh checks every file against its pin, then falls back to the source. Not part of the pipeline.

Test fixture fixture-v7

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at cdf8fb3; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v6

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at f2dbc26; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v5

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at 389a24b; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v4

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at 7c30e57; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v3

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at 98cb201; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v2

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at b08671a; see MANIFEST.txt and docs/testing.md.

Test fixture fixture-v1

Test data for the E2E workflow, not a pipeline release. A slice of the public GIAB HG002 genome, built by scripts/ci/build-fixture.sh at 5af372a; see MANIFEST.txt and docs/testing.md.

v0.8.2

What's Changed

• fix(pypgx): pin image to 0.26.0 to match the bundle (0.27.0 broke every gene)

Docker Images

All image versions are listed in versions.env.

To set up: ./scripts/setup.sh /path/to/data

v0.8.1

What's Changed

• fix(cnvpytor): restrict read-depth import to canonical chromosomes
• ci: use haplogrep3 trees (exit 0) for the smoke test
• ci: smoke-test the two digest-pinned images monthly

Docker Images

All image versions are listed in versions.env.

To set up: ./scripts/setup.sh /path/to/data