CLI Reference

Global Options

Search the bio.tools registry.

bc7 search <query> [OPTIONS]

Examples:

bc7 search "alignment"
bc7 search --operation "operation:0292"
bc7 search --topic genomics --limit 20
bc7 search "FASTQ" --format json

Get detailed information about a tool.

bc7 info <tool-id> [OPTIONS]

Examples:

bc7 info star
bc7 info salmon --format json

Generate a pipeline from natural language.

bc7 create <intent> [OPTIONS]

Option	Description
`--target` / `-t`	Pipeline target (`nextflow`, `snakemake`, `wdl`, `cwl`)
`--output` / `-o`	Output directory
`--validate`	Run validation after generation
`--heal`	Enable self-healing loops
`--containers`	Container type (`docker`, `singularity`)

Examples:

bc7 create "RNA-seq from FASTQ to differential expression" --target nextflow
bc7 create "variant calling pipeline" -t snakemake -o ./output/ --heal

Validate a pipeline file.

bc7 validate <path> [OPTIONS]

Option	Description
`--strict`	Enable strict validation
`--format`	Output format (`text`, `json`, `lsp`)

Get tool suggestions for a workflow.

bc7 suggest <task>

Generate a pipeline from explicit tool names.

bc7 generate <target> <tool1> <tool2> ...

Start the MCP server.

bc7 serve [OPTIONS]

Option	Description
`--transport`	Transport type (`stdio`, `http`)
`--port`	HTTP port (default: 3000)

Synchronize registry data.

bc7 sync <source> [OPTIONS]

Option	Description
`--incremental`	Only sync changes since last sync

Examples:

bc7 sync all
bc7 sync biotools
bc7 sync status

Manage configuration.

bc7 config show
bc7 config set <key> <value>

EDAM ontology utilities.

bc7 edam lookup <term> [--type operation|topic|data|format]
bc7 edam children <term>
bc7 edam parents <term>

Show version information.

bc7 version