The Agent Skills Directory

[SAFE]: The skill serves its stated purpose as a bioinformatics orchestrator. It uses industry-standard tools (STAR, Salmon, FastQC, MultiQC) and reputable community pipelines (nf-core).
[EXTERNAL_DOWNLOADS]: The skill instructions and scripts reference the installation of standard scientific Python and Conda packages (pandas, pytximport, pydeseq2, star, salmon, etc.) from official repositories (PyPI, Bioconda).
[REMOTE_CODE_EXECUTION]: The skill provides instructions for running the nf-core/rnaseq pipeline using Nextflow. This involves executing code from the well-known nf-core community repository, which is a standard and accepted practice in bioinformatics.
[COMMAND_EXECUTION]: The provided Python scripts (build_counts_matrix.py and validate_samplesheet.py) perform standard data processing tasks such as reading CSV/TSV files and writing results using pandas. They do not execute arbitrary shell commands or use dangerous subprocess calls.
[DATA_EXFILTRATION]: No evidence of unauthorized data access or external transmission was found. Network references are limited to legitimate tool downloads and remote FASTQ path validation logic.

bulk-rnaseq