The Agent Skills Directory

[COMMAND_EXECUTION]: The skill documentation includes numerous examples of executing bioinformatics tools (e.g., samtools, bwa) and system commands using Python's subprocess module and Bash scripts. This is the standard mechanism for orchestrating genomics pipelines on the DNAnexus platform.
[EXTERNAL_DOWNLOADS]: The skill guides users to install the dxpy library from PyPI and provides extensive instructions for managing application dependencies via system packages, Python requirements, and Docker images.
[DATA_EXFILTRATION]: The skill facilitates data movement (upload/download) between local environments and the DNAnexus cloud. All network operations are directed at the official platform infrastructure and are essential for the skill's operation.
[PROMPT_INJECTION]: As the skill involves processing genomics data files (FASTQ, BAM, VCF), it possesses an indirect prompt injection surface; however, this is a standard risk for tools processing untrusted input and is mitigated by the isolated nature of the platform's execution environment.
Ingestion points: Reads genomics data files and data objects from the DNAnexus platform (SKILL.md, data-operations.md).
Boundary markers: None identified in the provided code templates or documentation.
Capability inventory: Includes shell command execution via subprocess, file-write operations, and network access (app-development.md, configuration.md).
Sanitization: No specific data content validation or sanitization routines are mentioned in the references.

dnanexus-integration