# Dnanexus Integration

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy...

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-10-26
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration -g -a gemini-cli -y`

## Description

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Supports DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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 reviewed on **2026-09-30** against
`dxpy==0.415.0`, dxCompiler 2.18.0, and the 2026 DNAnexus documentation.
Consult `references/sources.md` and current release notes when behavior may
have changed. SDK signatures, CLI help, and offline validators were executed
locally; examples that transfer data, build, or launch workloads are illustrative
and require testing in the target account. No authenticated platform run was
performed during this review.

## Operating Contract

DNAnexus operations can expose regulated data, delete immutable objects, change
permissions, or incur compute and egress charges. Follow these rules:

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/dnanexus-integration/SKILL.md