The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill facilitates the download of sequencing data from the NCBI Sequence Read Archive (SRA) via official domains like sra-downloadb.be-md.ncbi.nlm.nih.gov. These are well-known scientific data services used as intended for genomic research.
[COMMAND_EXECUTION]: The workflow involves executing various bioinformatics command-line tools such as STAR, fastp, featureCounts, and samtools. These tools are invoked through the omicverse library's alignment module, which includes a feature to automatically resolve and install missing dependencies via conda or mamba.
[PROMPT_INJECTION]: The skill exhibits an indirect prompt injection surface as it is designed to ingest and process external data files including FASTQ, SRA, GTF, and FASTA.
Ingestion points: Data enters the environment via ov.alignment.prefetch, ov.alignment.fqdump, and ov.alignment.count from external URLs or local files.
Boundary markers: None observed in the instructions.
Capability inventory: The skill has the capability to execute shell commands for sequence processing and install packages via conda/pip.
Sanitization: The skill relies on the internal validation mechanisms of the bioinformatics tools it wraps (e.g., vdb-validate for SRA data).

bulk-fastq-quantification