/flow-bio

name: flow-bio
description: Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions,
  and check run status on any Flow instance.
license: MIT
metadata:
  version: 0.1.0
  author: ClawBio Contributors
  domain: bioinformatics
  tags:
  - flow
  - flow.bio
  - LIMS
  - pipelines
  - samples
  - nextflow
  - bioinformatics
  - cloud
  inputs:
  - name: reads1
    type: file
    format:
    - fastq
    - fq
    - fastq.gz
    - fq.gz
    description: First reads file for sample upload
    required: false
  - name: reads2
    type: file
    format:
    - fastq
    - fq
    - fastq.gz
    - fq.gz
    description: Second reads file for paired-end upload
    required: false
  outputs:
  - name: report
    type: file
    format: md
    description: Markdown report of Flow.bio interaction
  - name: result
    type: file
    format: json
    description: Machine-readable result envelope
  dependencies:
    python: '>=3.10'
    packages:
    - requests>=2.28
  demo_data:
  - path: data/demo_cache.json
    description: Pre-cached public Flow.bio data (pipelines, organisms, sample types) for offline demo
  endpoints:
    cli: python skills/flow-bio/flow_bio.py --demo --output {output_dir}
  openclaw:
    requires:
      bins:
      - python3
      env:
      - FLOW_URL
      - FLOW_TOKEN
    always: false
    emoji: 🌊
    homepage: https://flow.bio
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: requests
    trigger_keywords:
    - flow
    - flow.bio
    - flow bio
    - flow pipeline
    - flow sample
    - flow execution
    - flow project
    - flow upload
    - run on flow

Flow Bio Bridge

**ClawBio's gateway to the Flow.bio platform — browse, search, upload, and launch bioinformatics pipelines on Flow from the command line.**

Why This Exists

Flow.bio is a bioinformatics platform hosting curated Nextflow pipelines with managed compute, sample tracking, and collaborative project management. But interacting with Flow requires navigating the web UI or writing custom API scripts.

Flow Bio Bridge makes the platform **agent-accessible**: authenticate once, then list pipelines, upload samples, launch executions, and poll for results — all from the CLI or via the ClawBio orchestrator.

• **Without it**: Users must switch between web UI and local analysis, manually track execution IDs, and write one-off upload scripts
• **With it**: A single CLI covers discovery, upload, execution, and status checking across any Flow instance
• **Why ClawBio**: Chain Flow pipeline outputs with local ClawBio skills (e.g. Flow RNA-seq → ClawBio diffviz)

Core Capabilities

1. **Authentication** — Login via username/password, existing JWT token, or environment variables 2. **Pipeline discovery** — List and inspect available Nextflow pipelines with versions and parameter schemas 3. **Sample management** — List, search, and upload samples with metadata and organism tagging 4. **Project browsing** — List owned/shared projects and their contents 5. **Execution tracking** — Launch pipeline runs, poll status, and retrieve logs 6. **Search** — Full-text search across samples, projects, data, and executions 7. **Data listing** — Browse owned and shared data files 8. **Organism & type discovery** — List available organisms and sample types for uploads 9. **Overview mode** — Live overview of any Flow instance; public data without credentials, full account view with login

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | FASTQ (single-end) | `.fq`, `.fastq`, `.fq.gz` | reads1 | `sample_R1.fastq.gz` | | FASTQ (paired-end) | `.fq`, `.fastq`, `.fq.gz` | reads1, reads2 | `sample_R1.fastq.gz`, `sample_R2.fastq.gz` | | Any data file | any | — | annotation, reference, BED, etc. |

Workflow

When the user asks to interact with Flow.bio:

1. **Authenticate**: Use stored token, env vars, or prompt for credentials 2. **Discover**: List pipelines, sample types, organisms as needed 3. **Act**: Upload samples, launch executions, or query status 4. **Report**: Write structured output (JSON + markdown) to output directory 5. **Bundle**: Generate reproducibility commands and checksums

CLI Reference

# Login (stores token for subsequent calls)
python skills/flow-bio/flow_bio.py --login --username USER --password PASS
python skills/flow-bio/flow_bio.py --login --token TOKEN

# Discovery
python skills/flow-bio/flow_bio.py --pipelines
python skills/flow-bio/flow_bio.py --samples
python skills/flow-bio/flow_bio.py --projects
python skills/flow-bio/flow_bio.py --organisms
python skills/flow-bio/flow_bio.py --sample-types
python skills/flow-bio/flow_bio.py --executions
python skills/flow-bio/flow_bio.py --data

# Inspect details
python skills/flow-bio/flow_bio.py --execution EXEC_ID
python skills/flow-bio/flow_bio.py --sample SAMPLE_ID
python skills/flow-bio/flow_bio.py --pipeline PIPELINE_ID

# Inspect details via clawbio.py runner (uses --*-detail flags)
python clawbio.py run flow --execution-detail EXEC_ID
python clawbio.py run flow --sample-detail SAMPLE_ID
python clawbio.py run flow --pipeline-detail PIPELINE_ID

# Search
python skills/flow-bio/flow_bio.py --search "RNA-seq tumor"

# Raw JSON output (for piping to jq, etc.)
python skills/flow-bio/flow_bio.py --samples --json

# Upload sample
python skills/flow-bio/flow_bio.py --upload-sample \
  --name "Tumour_01" --sample-type "RNA-Seq" \
  --reads1 R1.fastq.gz --reads2 R2.fastq.gz \
  --organism "Homo sapiens" --project PROJECT_ID

# Launch pipeline
python skills/flow-bio/flow_bio.py --run-pipeline PIPELINE_VERSION_ID \
  --run-samples SAMPLE_ID1,SAMPLE_ID2 --output /tmp/flow_run

# Check execution status
python skills/flow-bio/flow_bio.py --execution EXEC_ID --output /tmp/flow_status

# Overview (public endpoints, no credentials needed)
python skills/flow-bio/flow_bio.py --demo --output /tmp/flow_demo