The Agent Skills Directory

[Local Script Execution]: The skill utilizes local Python scripts located in plugins/ngs-analysis/scripts/ to manage preflight checks and pipeline execution. These scripts are used to orchestrate standard bioinformatics tools (e.g., Nextflow, STARsolo). Contextually, these are internal components of the skill's infrastructure used to perform its primary function of data analysis.
[Integration with External Bioinformatics Tools]: The instructions reference well-known community-standard tools and frameworks such as nf-core/scrnaseq, STARsolo, kb-python, and alevin-fry. These are industry-standard resources for genomic analysis and their inclusion aligns with the skill's stated purpose of providing a count-generation workflow.
[Data Processing Surface]: The skill is designed to ingest and process various external data formats, including samplesheet.csv, FASTQ files, and matrix files (.h5, .h5ad, .rds). While processing external files is a standard security consideration for any data analysis tool, the skill includes explicit preflight and guardrail steps to ensure parameters and inputs are validated before execution.

ngs-scrna-seq