Status and Roadmap

Status and roadmap

The board. Everything MetaManifold claims to do is marked here as IN PLACE, PARTIAL, COMING or BLOCKED (legend on Home). Dates are Europe/London. The repository tree is the final arbiter; where this page and the code disagree, the code has moved and this page owes an update.

Pipeline — raw reads to tables

Capability	Status	Notes
cutadapt primer trimming (named primer pairs, IUPAC-validated)	IN PLACE	src/pipeline/tools.jl, config/primers.yml; UI editor under SYSTEM
DADA2 ASV lane: filter/trim, learn errors, denoise, merge, chimera cull, taxonomy	IN PLACE	src/pipeline/dada2/; R bridge pinned by renv.lock
SWARM OTU lane: merge, dereplicate, cluster, chimera check, vsearch taxonomy	IN PLACE	src/pipeline/swarm.jl, src/pipeline/vsearch stage
Optional cd-hit-est pre-clustering (multiplex inflation control)	IN PLACE	cdhit: config block
merge_taxa + named taxonomic filter sets	IN PLACE	src/pipeline/merge_taxa.jl, config/composition.yml library
Per-run DuckDB results store	IN PLACE	src/core/duckdb_store.jl
Stage freshness skipping (mtime for files, content hash for config)	IN PLACE	stale stages flagged with the exact changed keys
FastQC + MultiQC prefilter QC	PARTIAL	implemented and CI-exercised since #44; reports embed in the run view
Remote (SSH) offload of the taxonomy step	PARTIAL	works; authorisation is solely the operator's responsibility
DADA2 single-end / forward / reverse modes	IN PLACE	file_patterns.mode

Analysis and statistics

Capability	Status	Notes
Alpha diversity (richness, Shannon, Simpson) + group comparisons	IN PLACE	significance reports its status; never silently degrades (#31's rule)
Taxonomic composition bars; organism composition categories	IN PLACE	category sets editable in the UI
Taxon overlap (Euler/UpSet), pipeline-stage read summaries	IN PLACE
NMDS + PERMANOVA (vegan, locked R)	IN PLACE	permutation exchangeability is the standing caveat
Normalisation: none, rarefaction	IN PLACE
TSS/CSS/RSS size-factor offsets (exact, not aliases)	IN PLACE	issues #16, #61, #62 — conditions in docs/statistics/method-conditions/scaling-and-offsets.md
Exact descriptive summaries (counts, rational proportions)	IN PLACE	catalogue item 1; src/analysis/exact_summaries.jl
Numeric policy: exact / approximate / rounded, explicit modes	IN PLACE	src/analysis/numeric_policy.jl
Parametric fits — NB-GLM, CLR/ILR-LM, logistic (ML with refusal states)	PARTIAL	implemented with R-reference tests; independent statistical review (#1) outstanding
Zero-depth sample healing before transforms	IN PLACE	#58
Nonparametric tests (permutation/bootstrap)	COMING	catalogue item 3, approved scope only
Exact statistical tests (Fisher, exact NB, permutation PERMANOVA)	COMING	issue #3, catalogue item 4
Multinomial / Dirichlet-Multinomial regression	COMING	issue #17
Occupancy models, ZINB, hurdle	COMING	issue #18
Constrained ordinations (RDA/CCA/CAP/dbRDA)	COMING	issue #19
PhILR / SBP ILR bases, balance dendrograms	COMING	issue #20
Advanced zero handling (glmGamPoi dispersion, Bayesian multiplicative)	COMING	issue #21
ANCOM-BC, ALDEx2, Songbird-style methods	COMING	issue #5
Symbolic formula engine	BLOCKED	issue #2 — waits on real-data validation of the numeric layer

Workbench and application

Capability	Status	Notes
Config cascade (instance → study → group → run) + run_config.yml provenance	IN PLACE	UI editors at every level
Studies / groups / runs management, jobs panel, SSE live progress	IN PLACE
Results explorer (filters, presets, column presets, OTU drill-down, xlsx export)	IN PLACE
Functional annotation, consensus rank, contamination curation, FuncDB ledger	IN PLACE	composite confidence is explicitly curiosity-grade
Primers / databases / composition editors with validation and impact warnings	IN PLACE
CladeCumulus (cumulative cladistic explorer)	COMING	issue #6 — data structures and validation scaffolded (src/analysis/clade_cumulus.jl)
Full Evidence Mode (epistemic editor, fibre visualiser)	COMING	issue #7 — epistemic core in place (src/core/epistemic.jl)
Zenodo DOI minting	COMING	issue #8
Julia-authored Stipple/Vue UI	PARTIAL	first read-only slice landed; React remains default (docs/migration/STATUS.md)
Standalone offline release archives (Linux x64/ARM64, WSL2)	COMING	agreed requirement, no builder yet (docs/migration/STATUS.md)
Coordinated signed updater	COMING	same source
Multi-user / authenticated remote deployment	COMING	local single-user only until then — do not expose the server

Engineering estate

Capability	Status	Notes
Pinned toolchain (mise exact pins + Guix peer lane; sha256 pipeline tools)	IN PLACE	R is a documented system exception via renv.lock
Strict TypeScript estate (0 errors; unknown-safe stubs)	PARTIAL	skipLibCheck exception + alphaFig narrowing tracked in docs/compliance/fixme-index.md
Julia + frontend test suites, type-level assertions	IN PLACE	DOM-lane for Plotly-chain modules COMING (decision queued)
Benchmarks with baselines (informational lane)	IN PLACE	promotion to non-gating regression alert after a stability window
CI: hygiene, pinned tools, commit gate, Dependabot auto-merge-on-green	IN PLACE
Coverage gate	COMING	deliberate: gates on a recorded baseline, not an arbitrary number
OpenSSF Best Practices / Scorecard badges	COMING	enrolment first, badges on the day (never before)
Independent statistical review of the analysis layer	COMING	issue #1's acceptance gate; the reason PARTIAL marks exist above

Near-term order of work (as tracked)

1. Independent statistical review gate (#1) — unlocks the rest of the catalogue honestly.
2. Exact tests (#3) and the milestone-3 deferred suite (#17–21) in their approved dependency order (docs/issues/milestone3/).
3. Stipple UI parity and the standalone-release workstream (docs/migration/STATUS.md workstreams A and B).
4. CladeCumulus + Evidence Mode (#6–7), Zenodo (#8).
5. Symbolic engine (#2) only after the numeric layer is validated — the BLOCKED sign is policy, not neglect.

Reading the history

• Closed milestone issues mean the milestone closed, not "every deferred idea shipped" — deferred designs are preserved in docs/milestones/02-deferred-issues.md and docs/issues/milestone3/.
• Issues #1 and #2 are the two that must never be closed prematurely (the owner-review record makes this explicit).