The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill fetches the Salmon software binary from the official COMBINE-lab GitHub repository and downloads transcriptome reference data from the European Bioinformatics Institute (EBI) FTP servers. These are established and well-known sources in the scientific community.
[COMMAND_EXECUTION]: The skill utilizes shell commands to install Salmon via Conda, extract downloaded archives, and run the Salmon CLI for indexing and quantification. It also uses standard utilities like wget, grep, cat, and sed for data preparation.
[INDIRECT_PROMPT_INJECTION]: * Ingestion points: The skill processes external FASTQ files and transcript FASTA references, and later ingests Salmon's quantification output (quant.sf) into Python for downstream analysis. * Boundary markers: None present; the instructions assume the provided genomic files and tool outputs are formatted correctly and do not contain malicious content. * Capability inventory: The skill has the ability to execute shell commands (via Salmon and standard utilities) and write resulting data matrices to the local file system. * Sanitization: No specific sanitization or validation is performed on the transcript identifiers or quantification values before they are processed or used in analysis summaries.

salmon-rna-quantification