Usage Overview
py-gbcms can be used in two ways depending on your needs:
🔧 Standalone CLI (Single/Few Samples)
Best for:
Processing 1-10 samples
Quick ad-hoc analysis
Local development and testing
Direct control over parameters
Pros:
✅ Simple - just one command
✅ Fast to set up
✅ Full control over threading
✅ Works anywhere (local, server, container)
Cons:
❌ Manual parallelization for multiple samples
❌ No automatic resource management
❌ Requires manual error handling
Example:
Learn more: CLI Quick Start
🔄 Nextflow Workflow (Many Samples, HPC)
Best for:
Processing 10+ samples
HPC/SLURM cluster environments
Reproducible pipelines
Automated retry and error handling
Pros:
✅ Automatic parallelization across samples
✅ Smart resource management
✅ Built-in retry logic
✅ Resume failed runs
✅ Portable (Docker/Singularity)
Cons:
❌ Requires Nextflow installation
❌ More setup (samplesheet, config)
❌ Learning curve for Nextflow DSL
Example:
Learn more: Nextflow Workflow Guide
📊 Quick Comparison
Setup complexity
Low
Medium
Best for # samples
1-10
10+
Parallelization
Manual
Automatic
Resource management
Manual
Automatic
HPC integration
Manual
Built-in
Resume failed jobs
No
Yes
Reproducibility
Good
Excellent
Which Should I Use?
Use CLI if you:
Have a few samples to process
Want quick results
Are working locally or on a single server
Need full manual control
Use Nextflow if you:
Have many samples (10+)
Are on an HPC cluster (SLURM, PBS, etc.)
Need reproducible pipelines
Want automatic parallelization and error handling
Plan to re-run the analysis multiple times
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