alterlab-nf-core-sarek
Pass
Audited by Gen Agent Trust Hub on Sep 25, 2026
Risk Level: SAFEINDIRECT_PROMPT_INJECTIONEXTERNAL_DOWNLOADSCOMMAND_EXECUTIONREMOTE_CODE_EXECUTION
Full Analysis
- [INDIRECT_PROMPT_INJECTION]: The skill ingests data from local file systems which could be manipulated to influence agent behavior.\n
- Ingestion points: The
scripts/make_samplesheet.pyscript scans directories provided by the user to identify FASTQ files.\n - Boundary markers: No explicit delimiters are used to separate filenames from command instructions in the resulting CSV.\n
- Capability inventory: The skill utilizes
nextflow,python, and file system write operations.\n - Sanitization: The script performs regex-based validation of filenames, which limits the types of strings that can be processed.\n- [EXTERNAL_DOWNLOADS]: The skill references and executes workflows from external sources.\n
- Fetches the
nf-core/sarekpipeline version 3.8.1 from the nf-core community repository.\n - References genomic resource bundles (dbSNP, Mills/1000G indels) hosted by the Broad Institute.\n- [COMMAND_EXECUTION]: The skill provides templates for executing bioinformatics command-line tools such as
bwa-mem2,samtools, andgatk4. These commands are standard for genomic data processing and are restricted by theallowed-toolsconfiguration.\n- [REMOTE_CODE_EXECUTION]: The skill usesnextflowto download and run thenf-core/sarekworkflow. nf-core is an established community project for bioinformatics pipelines, and the execution is pinned to a specific release version (3.8.1).
Audit Metadata