The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill processes external biological data files and provides capabilities to execute platform jobs and local commands based on the contents of these files.
Ingestion points: The skill uses dxpy.download_dxfile and dxpy.find_data_objects to retrieve sequencing data and other data objects from the platform (seen in references/data-operations.md).
Boundary markers: No explicit boundary markers or instructions to ignore embedded content are defined for the ingested genomics data.
Capability inventory: The skill utilizes subprocess.check_call to run external bioinformatics tools and dxpy.DXApplet.run to launch cloud-based jobs (described in references/app-development.md and references/job-execution.md).
Sanitization: No specific sanitization or validation logic was identified for the content of the processed genomics files.
[COMMAND_EXECUTION]: The skill uses subprocess.check_call to execute bioinformatics tools and package managers within the execution environment.
Evidence: In references/configuration.md and references/app-development.md, the skill demonstrates using subprocess to call tools like samtools, bwa, and pip for processing data and managing dependencies within DNAnexus worker nodes.

alterlab-dnanexus