| name | analysis_to_slurm_runner |
| description | Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure. |
| category | bio/compute |
| version | 1 |
| requires_tools | ["search_knowledge_base","python_repl","write_file"] |
| requires_network | false |
| user_invocable | true |
| tags | ["slurm","pipeline","execution","hpc","runbook"] |
| aliases | ["slurm_analysis_planner"] |
| species | any |
| modality | compute |
| stage | reporting |
| stability | evolving |
| safety_level | medium |
Analysis to Slurm Runner
Purpose
Translate a biological analysis request into a cluster-oriented run plan, including Slurm assumptions, commands, and a draft script when appropriate.
When to use
Use this skill when the user wants to move from analysis planning to execution on an HPC cluster.
Required inputs
- analysis goal: what should be run
- toolchain (optional): python, R, scanpy, nextflow, custom script
- resource hints (optional): GPU, memory, CPUs, wall time
- output path (optional): where a script should be saved
Steps
- Search local compute or pipeline guidance with
search_knowledge_base.
- Infer the likely resource profile from the requested analysis.
- Use
python_repl to organize the run plan if needed.
- If a script is requested, draft a Slurm script or execution note using
write_file.
- Keep the output at the draft-plan level unless the user explicitly asks for a runnable script path.
Output format
- Run plan
- Resource assumptions
- Suggested command structure
- Optional script path
Failure modes
- Missing execution details: provide a conservative template and list assumptions.
- Unknown pipeline: ask the user what script or entrypoint should be run.
- Unsafe submission request: do not submit without the user's clear instruction.
Examples
- "Turn this scanpy workflow into a Slurm run plan."
- "Prepare a cluster script for a perturb-seq analysis job with 16 CPUs and 128G memory."
