AhmedHassan-bioinfo/OpenCare: OpenCare v1.0.0 — Paper snapshot

OpenCare v1.0.0 is a reproducible, containerized Nextflow (DSL2) workflow for paired tumor–normal exome processing and tumor-board-style review reporting. It runs end-to-end—from read QC to somatic calling, annotation, evidence enrichment, and deterministic report generation—producing an interactive HTML report and structured, versioned JSON exports designed for downstream integration and auditability.

Key features

End-to-end paired TN workflow (WES-focused): read QC, trimming, alignment, duplicate marking, somatic calling, annotation, reporting.

Tumor-board-style interactive HTML report: sortable/filterable prioritized variant view with explicit review warnings (incl. indel caution handling).

Structured JSON exports (versioned contract): report JSON as the single source of truth; HTML is rendered deterministically from JSON.

Offline-capable core path: local cached resources (e.g., Ensembl VEP cache and frozen CIViC snapshot) enable offline execution by default.

Optional online enrichment (explicit opt-in): OncoKB enrichment can be enabled when credentials/internet are available.

Reproducibility/provenance: captures tool versions, parameters, and runtime artifacts (trace/timeline/logs) via Nextflow.

Benchmarking included: SEQC2 HCC1395/HCC1395BL TN exome evaluation with stratified reporting by variant class and tumor VAF strata; indel evidence gating and length-stratified error analysis are supported.

What's new in this release

Stable TN exome "reporting-first" pipeline wiring with containerized tools

Default reporting rules and indel triage behavior refined for review workflows

Benchmark utilities for region-restricted evaluation and VAF stratification

Offline resource manifesting/checksums recorded in run metadata (where provided)