run-pipeline-safely

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

Run Pipeline Safely

When to use

User wants to run a bioinformatics pipeline or script and needs safe commands and directory setup.

Inputs

• pipeline: Name or path (e.g. "GEARS", "nextflow rnaseq").
• input_path, output_path: Optional; or user describes.

Steps

1. 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.

2. Hygiene: Suggest:

   • Create output directory with mkdir -p.
   • Use absolute or project-relative paths.
   • Avoid overwriting without confirmation; suggest dated or versioned output.

3. Command: Propose the run command (e.g. nextflow run ..., python main.py ...). Do not execute destructive commands; only suggest.

4. Checklist: Short list: (1) Output dir exists, (2) Paths checked, (3) Resource (slurm) if needed.

Output format

• Suggested commands (as text, not executed unless user confirms)
• Directory checklist
• One-line safety reminder