The Agent Skills Directory

[Command Execution]: The skill instructions include the execution of internal Python scripts (ngs_preflight.py and run_dna_umi_panel_variants.py) to manage Next-Generation Sequencing (NGS) workflows. These scripts are used to generate analysis plans and execute bioinformatics tools like samtools and bcftools locally. This is a standard practice for managing complex computational pipelines.
[File System Operations]: The skill reads from input files such as sample sheets, BED files, and reference genomes, and writes detailed quality control reports and environment configuration scripts (e.g., resource_env.sh) to the local file system. These operations are restricted to the directories specified in the workflow.
[Data Processing Considerations]: The skill processes external datasets including genomic sequencing files and sample metadata. While this represents a surface for indirect input, the workflow includes audit stages and preflight checks designed to validate inputs before full analysis execution.

ngs-dna-umi-panel-variants