snakemake-workflow-engine
Pass
Audited by Gen Agent Trust Hub on Jul 10, 2026
Risk Level: SAFECOMMAND_EXECUTIONEXTERNAL_DOWNLOADSREMOTE_CODE_EXECUTION
Full Analysis
- [COMMAND_EXECUTION]: The documentation demonstrates the use of the shell directive to automate bioinformatics tools like bwa and samtools, which is the standard and intended function of the Snakemake engine.
- [EXTERNAL_DOWNLOADS]: The skill provides instructions for installing the snakemake package via pip and conda, and includes rule examples for downloading reference datasets using wget.
- [REMOTE_CODE_EXECUTION]: The skill includes examples of executing bioinformatics tasks within remote Docker containers (e.g., gatk from the Broad Institute), ensuring reproducible environments via external code execution.
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