coloc plugin

Migrated from the legacy coloc_abf_container wrapper in nodes-io. One directory = one plugin family = one git-able unit. The family holds a single node kind, coloc_abf, backed by the official R coloc package (Wallace, CRAN 5.2.3, GPL-3.0-or-later).

Layout

• manifest.toml — node kind coloc_abf: 21 flattened params, ports, image provenance
• scripts/abf.sh — the execution script (R source despite the .sh name, matching the family convention; interpreter = "Rscript" in the manifest governs execution), inlined by the loader at startup
• Dockerfile — rocker/r-ver:4.5.1 + coloc 5.2.3 from CRAN Archive (moved verbatim from containers/coloc/)
• fixtures/coloc_abf_fixture.tsv — 10-SNP two-dataset smoke fixture
• test_coloc_abf.sh — build + smoke test (repointed to this directory)

The image contains only the official R package and its runtime; no reference panels, no LD matrices, no GWAS inputs are baked in. Reference: https://chr1swallace.github.io/coloc/

End-to-end workflow

./test_coloc_abf.sh     # builds localhost/atc/coloc:5.2.3 and smoke-tests it

Migration parity

The golden test (container-plugin/tests/coloc_migration.rs in the autonomics workspace) compares the compiled ContainerCommandSpec against the legacy Rust wrapper's output: image, command, outputs, resources, timeout, artifact prefix and panels are equal; the script differs structurally but preserves the exact invocation semantics.

Deltas introduced by the plugin architecture, all following the documented v0 patterns:

• Flattened dataset params. The legacy nested ColocDatasetSpec objects (dataset1.beta, ...) are scalar params (dataset1_beta, ...); the v0 param DSL has no object or enum types. The trait-type enum becomes a string param documented as quant or cc.
• Params travel via env. The legacy wrapper baked values into the R source with __PLACEHOLDER__ substitution; the plugin renders COLOC_* env values and the script reads them with Sys.getenv (optional fields gated by nzchar(), numbers via as.numeric()). The legacy wrapper had an empty env map; the compiled spec now carries the 21 rendered values.
• Cross-field validation moved into the script. Exactly one of (beta+varbeta) or pvalues, maf/n required with pvalues, s required for cc + pvalues, non-empty snp, and type in {quant, cc} were enforced by Rust validate() before the container started; the DSL cannot express them, so the script enforces the same rules with the same messages. Failures now surface inside the container instead of at node-build time. The p1/p2/p12 range check moved to DSL bounds (min = 0.0, max = 1.0).
• kind and artifact prefix drop the _container suffix (coloc_abf_container -> coloc_abf, /artifacts/coloc_abf). DAG specs referencing the old kind must be regenerated.