DNAnexus Integration
Purpose
Use this skill to build, run, and operate DNAnexus workloads without guessing at platform semantics. It covers:
dxCLI anddxpyautomation- 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:
- Start read-only. Confirm the user, project ID, region, folder, object IDs, and execution target before mutation.
- 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 oper…
