Usage Guide

# 1. Search for tools
bc7 search "RNA-seq alignment"
 
# 2. Create pipeline
bc7 create "RNA-seq from FASTQ to counts" --target nextflow
 
# 3. Validate
bc7 validate ./output/main.nf
 
# 4. Run (with Nextflow)
nextflow run ./output/main.nf

# Generate with automatic validation
bc7 create "variant calling from BAM files" \
  --target nextflow \
  --validate
 
# Generate with healing (auto-fix errors)
bc7 create "ChIP-seq peak calling" \
  --target snakemake \
  --heal

# Get suggestions, then choose tools manually
bc7 suggest "proteomics data analysis"
 
# Generate from specific tools
bc7 generate nextflow maxquant percolator flashlfq

# Generate pipelines for multiple targets
for target in nextflow snakemake wdl; do
  bc7 create "RNA-seq analysis" --target $target --output ./pipelines/$target/
done

You: "I need to analyze some RNA-seq data. Search for alignment tools."
Claude: [calls search_biotools] Found STAR, HISAT2, Bowtie2...

You: "Suggest a complete pipeline for RNA-seq differential expression"
Claude: [calls suggest_pipeline] Recommended workflow: FastQC → Trim Galore → STAR → featureCounts → DESeq2

You: "Generate this as a Nextflow pipeline"
Claude: [generates pipeline code using the suggested tools]

output/
├── main.nf              # Main pipeline file
├── nextflow.config      # Configuration
├── modules/             # Per-tool module definitions
│   ├── star.nf
│   ├── featurecounts.nf
│   └── deseq2.nf
├── manifest.json        # Provenance manifest
└── stub-test.log        # Stub test results