Usage Patterns

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:

gbcms run \
    --variants variants.vcf \
    --bam sample1.bam \
    --fasta reference.fa \
    --output-dir results/

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:

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    -profile slurm

Learn more: Nextflow Workflow Guide

---

📊 Quick Comparison

Feature	CLI	Nextflow
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