dnanexus-integration

1# DNAnexus Integration
2 
3## Purpose
4 
5Use this skill to build, run, and operate DNAnexus workloads without guessing
6at platform semantics. It covers:
7 
8- `dx` CLI and `dxpy` automation
9- Files, records, folders, projects, and metadata
10- Apps and applets defined by `dxapp.json`
11- Jobs, workflow analyses, retries, monitoring, and cost controls
12- Native workflows, WDL/CWL through dxCompiler, and Nextflow imports
13 
14The documented baseline was reviewed on **2026-09-30** against
15`dxpy==0.415.0`, dxCompiler 2.18.0, and the 2026 DNAnexus documentation.
16Consult `references/sources.md` and current release notes when behavior may
17have changed. SDK signatures, CLI help, and offline validators were executed
18locally; examples that transfer data, build, or launch workloads are illustrative
19and require testing in the target account. No authenticated platform run was
20performed during this review.
21 
22## Operating Contract
23 
24DNAnexus operations can expose regulated data, delete immutable objects, change
25permissions, or incur compute and egress charges. Follow these rules:
26 
271. Start read-only. Confirm the user, project ID, region, folder, object IDs,
28   and execution target before mutation.
292. Obtain confirmation before a billable launch, upload or download with
30   material egress, archive/unarchive request, deletion, project removal,
31   permission change, token revocation, or app publication unless the user
32   already explicitly requested that exact operation and target.
33…