dnanexus-integration
Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.
npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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
- Purpose
- Operating Contract
- Install and Authenticate
- Safe Preflight
- Choose the Right Path
- Core Workflows
- Transfer data
- Search accurately with dxpy
- Build an applet
- Launch with explicit controls
- Monitor jobs and analyses
- Chain executions without polling
- Current Platform Guidance
- Bundled Helpers
uv tool install "dxpy==0.410.0" dx --version uv add "dxpy==0.410.0" dx login dx whoami dx select dx pwd dx ls dx upload "sample.fastq.gz" \ dx download "project-xxxx:/results/sample.bam" \
What does the dnanexus-integration skill do?
Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill dnanexus-integration --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.