bringing the full-run json schema with versioning into the repo

Author: nrminor

.gitignore

@@ -134,6 +134,13 @@
 !/globus/scripts/*.sh
 !/globus/scripts/*.py
 
+# JSON report schemas
+!/schemas
+!/schemas/current
+!/schemas/v*
+!/schemas/v*/*.json
+!/schemas/v*/*.md
+
 # testing
 !/tests
 !/tests/data

schemas/current

@@ -0,0 +1 @@
+v0.1.0-alpha

schemas/v0.1.0-alpha/CHANGELOG.md

@@ -0,0 +1,34 @@
+# Schema Changelog
+
+## v0.1.0-alpha (Initial Alpha)
+
+Initial schema version for OneRoof reporting. Alpha version indicates
+the schema is experimental and breaking changes should be expected.
+
+### Top-level Structure
+
+- `schema_version`: Version string (e.g., "0.1.0-alpha")
+- `generated_at`: ISO 8601 timestamp
+- `run_metadata`: Pipeline run configuration and metadata
+- `summary`: Aggregate statistics across all samples
+- `samples`: Per-sample metrics keyed by sample_id
+
+### Sample Metrics
+
+Each sample includes:
+
+- `sample_id`: Unique identifier
+- `qc_status`: One of "pass", "warn", "fail"
+- `qc_notes`: Human-readable QC issue descriptions
+- `alignment`: Read mapping statistics
+- `variants`: Variant calling results (optional)
+- `consensus`: Consensus sequence metrics (optional)
+- `metagenomics`: Sylph profiling results (optional)
+- `haplotyping`: Devider haplotype phasing results (optional, Nanopore only)
+
+### QC Thresholds (defaults)
+
+- Coverage: pass ≥95%, warn ≥80%, fail <80% genome at ≥10x
+- Completeness: pass ≥98%, warn ≥90%, fail <90%
+- N percentage: pass <1%, warn <5%, fail ≥5%
+- Mapped reads: pass ≥1000, warn ≥100, fail <100