The Agent Skills Directory

Workflow Orchestration via Local Scripts: The skill utilizes local Python scripts located in the plugins/ngs-analysis/scripts/ directory to manage analysis tasks. These scripts act as wrappers for established tools such as GATK, samtools, and bcftools, facilitating preflight checks and workflow execution.
Data Ingestion and Processing: The skill is designed to process external genomic data, including FASTQ, BAM, and CRAM files, as well as sample sheets. This ingestion is central to its purpose in bioinformatics, where it parses metadata to generate command-line instructions.
Integration with Community Pipelines: The instructions recommend the use of nf-core/sarek for full workflows. This is a well-established community resource in the bioinformatics field for standardized pipeline execution.
Generation of Advisory Artifacts: During execution, the skill produces several local files, such as resource_plan.json and resource_env.sh, to document the analysis environment and resource readiness. This is a standard functional behavior for ensuring workflow reproducibility.

ngs-dna-germline-variants