dnanexus-integration

# DNAnexus Integration ## Purpose Use this skill to build, run, and operate DNAnexus workloads without guessing at platform semantics. It covers: - `dx` CLI and `dxpy` automation - Files, records, folders, projects, and metadata - Apps and applets defined by `dxapp.json` - Jobs, workflow analyses, retries, monitoring, and cost controls - Native workflows, WDL/CWL through dxCompiler, and Nextflow imports The documented baseline was verified on **2026-07-23** against `dxpy==0.410.0`, dxCompiler 2.17.0, and the 2026 DNAnexus documentation. Consult `references/sources.md` and current release notes when behavior may have changed. ## Operating Contract DNAnexus operations can expose regulated data, delete immutable objects, change permissions, or incur compute and egress charges. Follow these rules: 1. Start read-only. Confirm the user, project ID, region, folder, object IDs, and execution target before mutation. 2. Obtain confirmation before a billable launch, upload or download with material egress, archive/unarchive request, deletion, project removal, permission change, token revocation, or app publication unless the user already explicitly requested that exact operation and target. 3. Show resolved IDs and impact before destructive operations. Never infer a deletion target from a non-unique name. 4. Never print, log, return, or persist `DX_SECURITY_CONTEXT` or API tokens. Do not run `dx env` or `dx env --bash` in captured logs because both reveal the...