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LeonChaoX
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dnanexus-integration

Integrate DNAnexus applets and data workflows to run cloud analyses on FASTQ/BAM/VCF.

783|65|Updated Feb 27, 2026
Search Tags:#workflow orchestration#dxpy#dnanexus#genomics pipeline#dxapp.json#fastq bam vcf#upload download
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill dnanexus-integration-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/13-%E5%AE%9E%E9%AA%8C%E5%AE%A4%E8%87%AA%E5%8A%A8%E5%8C%96%E4%B8%8E%E9%9B%86%E6%88%90/dnanexus-integration
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill dnanexus-integration-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill helps you integrate your genomics and bioinformatics workflows with the DNAnexus cloud platform, so you can reliably build apps/applets, manage sequencing data, and run end-to-end analyses at scale.

Core Features & Use Cases

  • App/Applet development: Scaffold and implement Python/Bash executables with proper inputs/outputs, then build and deploy to DNAnexus.
  • Data operations: Upload/download, search, organize FASTQ/BAM/VCF files and records, and manage projects, folders, and permissions.
  • Execution orchestration: Launch jobs and workflows, monitor status/logs, chain multi-step pipelines, and handle parallel processing.

Quick Start

Use the dnanexus-integration Skill to build a DNAnexus applet that uploads a FASTQ input, runs a quality filtering command inside the app, and returns the filtered reads as an output link using dxpy.

Frequently Asked Questions about dnanexus-integration

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate a genomics pipeline on DNAnexus using dxpy?▼

Automate genomics pipelines on DNAnexus by integrating the dxpy Python SDK to configure dxapp.json, manage FASTQ/BAM/VCF data objects, and execute deterministic cloud analyses. This enables programmatic job orchestration and workflow chaining at scale.

How do I build and deploy a DNAnexus applet from scratch?▼

Build and deploy a DNAnexus applet by scaffolding Python or Bash executables, defining inputs and outputs, configuring dxapp.json dependencies, and running the deployment commands. This ensures deterministic app execution with managed project data objects.

Can I use dxpy to upload and manage FASTQ files in DNAnexus projects?▼

Upload and manage FASTQ files in DNAnexus projects using the dxpy Python SDK for data operations. The integration supports uploading, downloading, searching, and organizing sequencing records while managing project folders and permissions.

What is needed to run deterministic DNAnexus workflows for cloud analyses?▼

Running deterministic DNAnexus workflows requires dx login authentication, correct dxapp.json configuration, dxpy integration, and properly managed FASTQ/BAM/VCF inputs and outputs. This setup ensures reliable end-to-end cloud analyses and multi-step pipeline chaining.

Does DNAnexus integration support chaining multi-step bioinformatics jobs?▼

DNAnexus integration supports chaining multi-step bioinformatics jobs by launching workflows, monitoring status and logs, and handling parallel processing. This allows you to reliably run end-to-end cloud analyses on sequencing data at scale.

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