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Propose safe commands and directory hygiene for running a pipeline.
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Basierend auf der SOC-Berufsklassifikation
Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.
| name | run_pipeline_safely |
| description | Propose safe commands and directory hygiene for running a pipeline. |
| category | bio/compute |
| version | 1 |
| requires_tools | ["terminal","read_file"] |
| requires_network | false |
| user_invocable | true |
| species | any |
| modality | compute |
| stage | utilities |
| stability | experimental |
| safety_level | medium |
User wants to run a bioinformatics pipeline or script and needs safe commands and directory setup.
Clarify: Identify input/output dirs and whether they are on shared storage (e.g. GPFS). Prefer output to a project or scratch dir, not home if large.
Hygiene: Suggest:
Command: Propose the run command (e.g. nextflow run ..., python main.py ...). Do not execute destructive commands; only suggest.
Checklist: Short list: (1) Output dir exists, (2) Paths checked, (3) Resource (slurm) if needed.
