The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill fetches installation scripts from the official domains for Nextflow (https://get.nextflow.io) and nf-test (https://get.nf-test.com).\n- [COMMAND_EXECUTION]: The skill uses a shell pipe to execute remote scripts (curl | bash) for the setup of the Nextflow runtime and nf-test framework, which are standard installation methods for these tools.\n- [COMMAND_EXECUTION]: The instructions recommend using sudo to move the Nextflow executable to a system-wide path (/usr/local/bin/), which is a common administrative task for CLI tool deployment.\n- [EXTERNAL_DOWNLOADS]: Software management is performed through reputable registries, including the installation of nf-core via pip and various workflow dependencies via the Bioconda and Conda-forge channels.\n- [REMOTE_CODE_EXECUTION]: The skill facilitates an indirect injection surface by teaching the agent to ingest external CSV data which is subsequently used in shell command construction.\n
Ingestion points: Data enters the environment from CSV samplesheets processed with splitCsv in references/language.md.\n
Boundary markers: There are no markers or instructions provided to distinguish between data and potential commands within the processed files.\n
Capability inventory: Nextflow process blocks execute arbitrary Bash scripts using variables interpolated from the ingested data, as demonstrated in references/language.md.\n
Sanitization: No input validation or escaping procedures are described for the data extracted from samplesheets before it is used in command execution.

nextflow