mtag plugin

Migrated from the legacy mtag_container wrapper in nodes-io. One directory = one plugin family = one git-able unit.

Layout

• manifest.toml — node kind mtag: params, ports, panel binding, image provenance
• scripts/h2.sh — the execution script, referenced relatively and inlined by the loader at startup
• Dockerfile — image build provenance (moved verbatim from containers/mtag/; the build context is this directory, since the Dockerfile COPYs mtag/… paths; build + push still via GHCR)
• .dockerignore — moved verbatim
• mtag/ — vendored upstream JonJala/mtag source as plain files (the embedded .git was stripped per the plugin-migration workflow; the upstream commit is pinned in the Dockerfile org.opencontainers.image.revision label, the manifest upstream field, and test_mtag_containers.sh)
  • mtag/ld_ref_panel/eur_w_ld_chr/ — the official 1000G EUR eur_w_ld_chr w-LD scores used to build and publish the catalog bundle wjixiang/catalog-mtag-ld-ref-1000g-eur-w-ld (input to the panel-publishing flow only; runtime panel mounts resolve through the catalog, never this tree)
• make_baseline_fixture.py — deterministic two-trait baseline generator for the end-to-end test
• test_mtag_containers.sh — image + panel + E2E baseline; root= repointed to this directory. The catalog and Rust-E2E steps invoke cargo, so run it from the autonomics workspace checkout (the cargo invocation targets nodes-io --test container_file_flow real_catalog_backed_official_mtag_runs_in_podman, which still registers the legacy wrapper factory until the wrapper is deleted)
• fixtures/ — generated baseline notes (outputs are not committed)

Provenance

• Image: ghcr.io/auto-nomics/autonomics/mtag@sha256:28ac0a0a0ee741340390b7588bf8ba36e6b316d62adc0cab7fd4494f5dd6a90c, tag 1.0.8, from Dockerfile (base python:2.7.18-slim-buster with a bitarray==0.8.1 builder stage).
• Upstream: JonJala/mtag 1.0.8 at revision 9e17f3cf1fbcf57b6bc466daefdc51fd0de3c5dc; license GPL-3.

Migration parity

The golden test (crates/container-plugin/tests/mtag_migration.rs) compares the compiled ContainerCommandSpec against the legacy Rust wrapper: image, outputs, panel bundle, resources, timeout, and command are equal; the script differs structurally (env-driven optional flags instead of Rust string building) but preserves the exact official invocation tokens and flag order. Deliberate deltas:

• Kind rename: mtag_container → mtag; the artifact prefix follows the kind (/artifacts/mtag_container → /artifacts/mtag). DAG specs referencing the old kind must be regenerated.
• timeout_secs / artifact_prefix are node-level constants (3600 s, /artifacts/mtag) instead of per-instance spec params; the legacy spec accepted per-node overrides, the plugin DSL does not.
• Params travel via env (MTAG_*). time_limit_hours and tol always render (defaults 1.0 and 1e-6); the six official boolean flags are optional = true and are tested with [ -n "$VAR" ], so an omitted param means the flag is left off exactly like the legacy if spec.force { push("--force") }. Nuance inherited from the ldsc-munge pattern: explicitly submitting false renders "false" (non-empty) and therefore appends the flag — the schema steer is to omit a flag rather than submit false.
• Cross-field rule via the DSL: equal_h2 = { requires = ["perfect_gencov"] } — the compile-time check_requires gate enforces the legacy validate() rule ("equal_h2 requires perfect_gencov") at spec-compile time; mtag is the first family to use the gate, so no script-side guard exists.
• Numbers render with the serde_json spelling: 1.0 → "1.0" (legacy format! produced "1"), 1e-6 → "1e-6" (legacy produced "0.000001"). Equal after float parsing, which is what the official argparse float does (documented pitfall 8).
• No gzip stanza, on purpose: the legacy mtag script passed both inputs straight through (no decompress_gzip_inputs helper), so the plugin script does too — plain TSV is expected, unlike ldsc.
• validate() coverage: time_limit_hours/tol finite and > 0 → exclusive_min = 0.0; timeout_secs > 0 and the absolute artifact_prefix are enforced by loader validation; two File inputs and the three outputs match the legacy port layout and formats (mtag_results × 2, mtag_log).
• Test-script deltas: root= repointed to this directory; the git submodule update guard and git -C … rev-parse commit probe were replaced by a static upstream pin (the vendored .git is stripped); the dead AUTONOMICS_MTAG_IMAGE_PREFIX export was dropped (no reader anywhere in crates/).