Workflows

This page lists the safe and destructive patterns in the Workflow Engines shell guard pack. See Shell Tool for how these patterns are evaluated.

Workflow Engines

Pack ID: workflows.engines

Guards against destructive operations in scientific workflow engines

Safe patterns

Rule ID	Pattern
`workflows.engines.nextflow_log`	`^nextflow\s+log\b[^\|><]*$`
`workflows.engines.nextflow_list`	`^nextflow\s+list\b[^\|><]*$`
`workflows.engines.snakemake_summary`	`^snakemake\s+--summary\b[^\|><]*$`
`workflows.engines.snakemake_dryrun`	`^snakemake\s+(?:--dryrun\|-n\|--dry-run)\b[^\|><]*$`

Destructive patterns

Rule ID	Reason	Suggestion	Confidence
`workflows.engines.nextflow_clean`	Removes cached workflow data and intermediate results	Use `nextflow log` to review runs before cleaning	Medium
`workflows.engines.nextflow_drop`	Removes a cached pipeline from local storage	Use `nextflow list` to review cached pipelines first	Medium
`workflows.engines.snakemake_delete_all`	Deletes all output files produced by the workflow	Review outputs with `snakemake --summary` first	High
`workflows.engines.snakemake_unlock`	Force-unlocks a workflow directory, risking concurrent execution conflicts	Ensure no other Snakemake instance is running first	Medium

This documentation was generated from rust/agents/src/tool_guard/shell/packs/workflows.rs.

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