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Getting Started

This guide will help you get started with the Flow platform.

Overview

Flow is organized around organizations and projects:

  • Organizations - Groups of users (e.g., research labs, departments)
  • Projects - Workspaces for files and workflows within an organization

You can use Flow through the web interface or the command-line tool (CLI).

Web Interface

Step 1: Log In

  1. Navigate to the Admin Console: admin.flow.labpgx.com
  2. Click Login to authenticate with your credentials
  3. If you don't have an account, contact your organization administrator

Step 2: Select Your Organization

After logging in, you'll see your available organizations.

Organizations List

Click on an organization to select it as your current context.

Step 3: Select a Project

Once an organization is selected, you'll see its projects.

Projects List

Click on a project to set it as your current working context.

Step 4: Browse Files

With a project selected, navigate to the File Browser to access your data:

File Browser

Here you can:

  • Browse cloud storage (GCS or S3)
  • Download files
  • Navigate folder hierarchies

Step 5: Run a Workflow

Navigate to the Compute service to run bioinformatics pipelines:

Compute Dashboard

Command Line Interface

The CLI provides powerful command-line access to all Flow features.

Step 1: Install

pip install iseq-flow

Step 2: Authenticate

Get a Personal Access Token (PAT) from the Admin Console under Settings > CLI Tokens.

flow login --token YOUR_PAT_TOKEN

Verify your login:

flow status

Step 3: Select Project

Select a default project for all commands:

flow config select-project

This shows an interactive menu:

Available Projects

Intelliseq
  [1] Demo Project
  [2] Clinical Lab

Partner Org
  [3] Research Project

Enter project number (or 'q' to cancel): 1

Selected project: Demo Project
  Organization: Intelliseq
  Project ID: abc123-def456-...

Step 4: Browse Files

# List files in project root
flow files ls

# List files in subdirectory
flow files ls data/samples

# Download a file
flow files download data/sample.vcf

# Upload a file
flow files upload local_file.vcf data/remote_file.vcf

Step 5: Run a Workflow

# List available pipelines
flow pipelines list

# Submit a pipeline run (paths are relative to project bucket)
flow runs submit --pipeline hereditary-mock \
  -P case_id=case-001 \
  -P child_fastq=data/R1.fastq.gz \
  -P child_fastq=data/R2.fastq.gz \
  --watch

# List runs
flow runs list

# Check run status
flow runs status RUN_ID

Step 6: Manage Orders (Clinical Workflows)

# Create a clinical order
flow orders create -n "Patient Case 001" \
  --priority urgent \
  --indication "Family history of cancer"

# List orders
flow orders list

# Associate a run with an order
flow runs submit --pipeline hereditary-mock \
  --order-id ORDER_ID \
  -P case_id=case-001 \
  --watch

Next Steps