Pin snpeff=5.1 (log4j 2.17.1, openjdk 8); add vuln management docs to AGENTS.md

snpeff 5.1 already bundles log4j-core 2.17.1 (Log4Shell fix) and uses
openjdk 8, avoiding the ARM64 icu solver conflict from 5.2+.

Add Container Vulnerability Management section to AGENTS.md covering:
- Trivy scanning setup (Rego policy, .trivyignore, JSON artifacts)
- Common vulnerability sources (Java fat JARs, Go binaries, vendored deps)
- ARM64 solver conflict patterns and mitigations
- CVE triage decision process

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: dpark01

AGENTS.md

@@ -147,6 +147,7 @@ viral-ngs/
 │       ├── core.txt
 │       ├── core-x86.txt        # x86-only core packages
 │       ├── assemble.txt
+│       ├── assemble-x86.txt    # x86-only assembly packages
 │       ├── classify.txt
 │       ├── classify-x86.txt    # x86-only classify packages
 │       ├── phylo.txt
@@ -503,6 +504,75 @@ micromamba search -c bioconda <package> --subdir linux-aarch64
 
 ---
 
+## Container Vulnerability Management
+
+### Scanning
+
+Container images are scanned for vulnerabilities using [Trivy](https://aquasecurity.github.io/trivy/):
+
+- **On every PR/push**: `docker.yml` scans each image flavor after build (SARIF → GitHub Security tab, JSON → artifact)
+- **Weekly schedule**: `container-scan.yml` scans the latest published images
+- Scans filter to **CRITICAL/HIGH** severity, **ignore-unfixed**, and apply a Rego policy (`.trivy-ignore-policy.rego`)
+- Per-CVE exceptions go in `.trivyignore` with mandatory justification comments
+
+### Rego Policy (`.trivy-ignore-policy.rego`)
+
+The Rego policy filters CVEs that are architecturally inapplicable to ephemeral batch containers:
+
+- **AV:P** (Physical access required) — containers are cloud-hosted
+- **AV:A** (Adjacent network required) — no attacker on same network segment
+- **AV:L + UI:R** (Local + user interaction) — no interactive sessions
+- **AV:L + PR:H** (Local + high privileges) — containers run non-root
+- **AV:L + S:U** (Local + scope unchanged) — attacker already has code execution and impact stays within the ephemeral container
+
+Changes to this policy should be reviewed carefully. The comments in the file explain the rationale and risk for each rule.
+
+### Common Vulnerability Sources
+
+**Python transitive deps**: Pin minimum versions in `docker/requirements/*.txt`. Prefer conda packages over pip. Check conda-forge availability before assuming a version exists — conda-forge often lags PyPI by days/weeks.
+
+**Java fat JARs** (picard, gatk, snpeff, fgbio): Bioinformatics Java tools are distributed as uber JARs with all dependencies bundled inside. Trivy detects vulnerable libraries (log4j, commons-compress, etc.) baked into these JARs. Version bumps can cause ARM64 conda solver conflicts because Java tools pull in openjdk → harfbuzz → icu version chains that clash with other packages (r-base, boost-cpp, pyicu). Always check:
+1. Whether the tool is actually flagged by Trivy (don't bump versions unnecessarily)
+2. Whether the CVE applies (e.g., log4j 1.x is NOT vulnerable to Log4Shell)
+3. Whether the desired version resolves on ARM64 before pushing
+
+**Go binaries**: Some conda packages bundle compiled Go binaries (e.g., mafft's `dash_client`, google-cloud-sdk's `gcloud-crc32c`). If the binary is unused, delete it in the Dockerfile. Delete from **both** the installed location and `/opt/conda/pkgs/*/` (conda package cache) — Trivy scans the full filesystem.
+
+**Vendored copies**: Packages like google-cloud-sdk and setuptools bundle their own copies of Python libraries that may be older than what's in the conda environment. Trivy flags these vendored copies separately. Options: delete the vendored directory (if not needed at runtime), or accept the risk in `.trivyignore` with justification.
+
+### ARM64 Solver Conflicts
+
+The conda solver on ARM64 (linux-aarch64) is more constrained than amd64 because fewer package builds exist. Common conflict patterns:
+
+- **icu version conflicts**: Many packages (openjdk, r-base, boost-cpp, pyicu) pin specific icu version ranges. Bumping one package can make the entire environment unsolvable.
+- **libdeflate/htslib conflicts**: lofreq 2.1.5 pins old htslib/libdeflate versions that conflict with newer pillow/libtiff.
+- **openjdk version escalation**: snpeff 5.2+ requires openjdk>=11, 5.3+ requires openjdk>=21. Higher openjdk versions pull in harfbuzz→icu chains that conflict with everything.
+
+When a solver conflict occurs: revert the change, check what version the solver was picking before, and pin to that exact version if it already addresses the CVE.
+
+### Mitigation Decision Process
+
+When triaging a CVE:
+
+1. **Check the CVSS vector** — does the Rego policy already filter it?
+2. **Identify the source package** — use Trivy JSON output (`PkgName`, `PkgPath`, `InstalledVersion`)
+3. **Check if a fix version exists on conda-forge/bioconda** — not just on PyPI
+4. **Test on ARM64** — solver conflicts are the most common failure mode
+5. **If the fix version conflicts**: consider whether the CVE is exploitable in your deployment model. Document the risk assessment in `.trivyignore` or `vulnerability-mitigation-status.md`.
+6. **If the vulnerable code is unused**: delete the binary/file inline in the Dockerfile (same RUN layer as install to avoid bloating images)
+
+### Key Files
+
+| File | Purpose |
+|------|---------|
+| `.trivy-ignore-policy.rego` | Rego policy for class-level CVE filtering |
+| `.trivyignore` | Per-CVE exceptions with justifications |
+| `.github/workflows/docker.yml` | Build-time scanning (SARIF + JSON) |
+| `.github/workflows/container-scan.yml` | Weekly scheduled scanning |
+| `vulnerability-mitigation-status.md` | Local-only tracking doc (not committed) |
+
+---
+
 ## Troubleshooting
 
 ### Circular Import Errors

docker/requirements/phylo.txt

@@ -4,5 +4,5 @@ lofreq>=2.1.5
 mafft>=7.508
 mummer4>=4.0.0rc1
 muscle=3.8.1551
-snpeff>=4.3.1t
+snpeff=5.1
 vphaser2>=2.0

src/viral_ngs/phylo/snpeff.py

@@ -23,7 +23,7 @@
 _log = logging.getLogger(__name__)
 
 TOOL_NAME = 'snpEff'
-TOOL_VERSION = '4.3.1t'
+TOOL_VERSION = '5.1'
 
 
 class SnpEff(core.Tool):