The Agent Skills Directory

[COMMAND_EXECUTION]: The skill uses shell commands and the subprocess.run Python function to execute cnvkit.py and other bioinformatics utilities like samtools and Rscript. These operations are consistent with the skill's stated purpose of automating genomic analysis pipelines.
[EXTERNAL_DOWNLOADS]: The skill provides instructions to download and install software and dependencies from official, well-known registries including PyPI (pip install cnvkit), Bioconda (conda install -c bioconda cnvkit), and Bioconductor (BiocManager::install("DNAcopy")). These sources are recognized as safe environments for package distribution.
[INDIRECT_PROMPT_INJECTION]: The skill exhibits an attack surface for indirect prompt injection as it ingests and processes untrusted external genomic data.
Ingestion points: Processes user-provided BAM, BED, and FASTA files, as well as intermediate CNVkit data files (CNN, CNR, CNS) as described in Steps 2-8.
Boundary markers: No specific boundary markers or instruction-ignoring delimiters are employed when processing or outputting data from these files.
Capability inventory: The skill possesses the ability to execute shell commands via subprocess.run and perform file system operations through the cnvlib and pandas libraries.
Sanitization: No explicit sanitization or validation of the content within the genomic data files is documented before it is processed by the analysis tools.

cnvkit-copy-number