Adding Tools

Overview

BioContext7 discovers tools automatically from bio.tools, nf-core, and Bioconda. You can also register custom tools using a biocontext7.json manifest file and declare crawl-time metadata for GitHub repositories with biocontext7.yaml.

Repository Metadata via biocontext7.yaml

If your tool lives on GitHub, add a biocontext7.yaml file at repository root to override auto-extracted metadata during documentation crawling.

# biocontext7.yaml (repository root)
name: DESeq2
description: Differential gene expression analysis based on the negative binomial distribution
language: [R]
edam_operations: ["operation:3223"]
edam_topics: ["topic:3308"]
documentation:
  - url: https://bioconductor.org/packages/DESeq2/
    type: reference
  - url: https://bioconductor.org/packages/DESeq2/vignettes/DESeq2.html
    type: vignette
citation:
  doi: "10.1186/s13059-014-0550-8"
deprecated: false

biocontext7.yaml Schema

Field	Type	Required	Notes
`name`	`string`	No	Author-preferred tool display name
`description`	`string`	No	Author-preferred summary
`language`	`string[]`	No	Programming languages
`edam_operations`	`string[]`	No	Must match `operation:NNNN`
`edam_topics`	`string[]`	No	Must match `topic:NNNN`
`documentation`	`[{ url, type }]`	No	Preferred docs URLs (higher priority than auto URLs)
`citation.doi`	`string`	No	DOI format `10.XXXX/...`
`deprecated`	`boolean`	No	Author-declared deprecation state

Malformed biocontext7.yaml files are rejected by schema validation and ignored for overrides. Valid files take precedence over auto-extracted metadata for supported fields.

The biocontext7.json Manifest

Create a biocontext7.json file in your tool's root directory:

{
  "name": "my-custom-tool",
  "version": "1.0.0",
  "description": "A custom bioinformatics tool",
  "operations": ["operation:0292"],
  "topics": ["topic:3308"],
  "inputs": [
    {
      "data": "data:2044",
      "format": "format:1930",
      "description": "Input FASTQ files"
    }
  ],
  "outputs": [
    {
      "data": "data:0863",
      "format": "format:2573",
      "description": "Aligned BAM file"
    }
  ],
  "container": {
    "docker": "myregistry/my-tool:1.0.0",
    "singularity": "docker://myregistry/my-tool:1.0.0"
  },
  "command": "my-tool align --input {input} --output {output}",
  "documentation": "https://my-tool.readthedocs.io"
}

Manifest Fields

Field	Required	Description
`name`	Yes	Unique tool identifier
`version`	Yes	Semantic version string
`description`	Yes	Short description of the tool
`operations`	Yes	EDAM operation URIs
`topics`	No	EDAM topic URIs
`inputs`	Yes	Input data types and formats (EDAM)
`outputs`	Yes	Output data types and formats (EDAM)
`container`	No	Docker/Singularity image references
`command`	No	Command template with `{input}` / `{output}` placeholders
`documentation`	No	URL to tool documentation

EDAM Ontology Terms

Use EDAM terms to describe your tool's operations, topics, and data types. You can look up terms using the CLI:

# Look up operations
bc7 edam lookup "sequence alignment"
 
# Look up topics
bc7 edam lookup --type topic "genomics"
 
# Look up data types
bc7 edam lookup --type data "sequence"

Register a Custom Tool

# Register from a manifest file
bc7 register ./biocontext7.json
 
# Register from a directory (auto-discovers biocontext7.json)
bc7 register ./my-tool/
 
# Verify registration
bc7 info my-custom-tool

Register via Python API

from bio_pipeline_maker.registry import ToolRegistry
 
registry = ToolRegistry()
 
await registry.register_tool({
    "name": "my-custom-tool",
    "version": "1.0.0",
    "description": "A custom bioinformatics tool",
    "operations": ["operation:0292"],
    "inputs": [{"data": "data:2044", "format": "format:1930"}],
    "outputs": [{"data": "data:0863", "format": "format:2573"}],
})

Tool Discovery Pipeline

When BioContext7 resolves tools for a pipeline, it searches in order:

Local registry — custom tools registered via biocontext7.json
nf-core modules — community-curated Nextflow modules (if prefer_nfcore is enabled)
bio.tools — 47,000+ tools with EDAM semantic matching
BioContainers — container image resolution for reproducibility

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