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About the Common Workflow Language
About the Common Workflow Language
GET STARTED
About the Seven Bridges Platform
Time synchronization
Before you start
QuickStart
Account settings
About the Payments page
Manage your subscription
Cloud infrastructure pricing
Compute costs
Storage costs
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Developer Dashboard
Email notifications page
TUTORIALS
Seven Bridges Platform tutorials
Build a workflow tutorial
Worked example of uploading SAMtools Sort
Upload a custom Python program using a Dockerfile
Create a tar archive
Troubleshooting tutorial
Comprehensive tips for reliable and efficient analysis set-up
ACCESS THE SEVEN BRIDGES PLATFORM
Sign up for the Seven Bridges Platform
Access via the visual interface
Access via the API
Set up two-factor authentication
MANAGE AN ANALYSIS ENVIRONMENT
Projects on the Seven Bridges Platform
Create a project
View a project
Manage the project dashboard
Modify project settings
Set file download restriction
Manage email notifications
Add notes to your project
Leave a project
Delete a project
Tag your projects
COLLABORATE SECURELY
Collaboration on the Seven Bridges Platform
Add a collaborator to a project
Set permissions
DATASETS HUB
About datasets
BRING YOUR PRIVATE DATA
Upload your data to the Seven Bridges Platform
Upload from your computer
Upload via the command line
Import from an FTP/HTTP(S) server
Upload via the API
Import from a Volume
Import from a DRS server
SET METADATA ASSOCIATED WITH A FILE
Metadata on the Seven Bridges Platform
System metadata
Metadata schema
Edit metadata using the visual interface
Edit metadata with a manifest
Export metadata to a manifest
Edit metadata using the command line uploader
Edit metadata using the API
Metadata manifest file format
SEARCH FILES
File repositories on the Seven Bridges Platform
Search files on the Platform
ADD FILES TO A PROJECT
Add files using the visual interface
Copy files using the API
Tag your files
ORGANIZE FILES
Available actions
Activity center
New File Browser
ARCHIVE FILES (on AWS)
File archiving overview
Archive a file
Restore a file
Delete an archived file
ARCHIVE APPS
App archiving overview
Archive an app
Restore an app
SBFS (Beta)
About SBFS
Install SBFS automatically
Install SBFS manually
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
Command reference
Configure
List
Mount
Actions after mounting
Unmount
General commands
SBFS Log
Upgrade SBFS
Uninstall SBFS
FIND APPS
Apps on the Seven Bridges Platform
Publish a third-party app or workflow
Search for an app
Explore app details
App versions
Interactive Web Apps
BRING YOUR TOOLS
About the SDK
About the Common Workflow Language
CWL v.1.0 improvements over sbg:draft-2
CWL v1.2 conditional execution
Bring Nextflow apps to the Platform
Add Nextflow apps through the command line interface (CLI)
Add Nextflow apps through the visual interface
Manage Nextflow apps on the Platform
Set execution mode for Nextflow apps
sbpack_nf command reference
Nextflow Quickstart Tutorial
Nexttflow CLI app upload tutorial
Using Sample Sheets with Nextflow Apps on the SevenBridges Platform
Important Points
Bring WDL apps to the Platform
DOCKER
About Docker
Install Docker
Install Docker on Linux
Install Docker on macOS
Install Docker on Windows
Image registries
About the Seven Bridges Image Registry
About Docker Hub
Create and upload a Docker image
Create and upload a Docker image with a Dockerfile
Manage Docker repositories
Core Docker commands
Docker for Enterprise
Mount a USB drive in a Docker container
Docker best practice recommendations
DESCRIBE YOUR TOOL (LEGACY)
The Tool Editor
General tool information
Tool input ports
Tool output ports
Additional tool information
Test the tool description
Dynamic Expressions in Tool Descriptions
Advanced features of the tool editor
Forking tools
TOOL WRAPPING TIPS AND TRICKS
Tips and tricks
Make files available in your tool's working directory
Set the default value for an input port
JavaScript Cookbook
Set suggested input values for CWL v1.x apps
COPY AN APP
Copy public apps to a project
Copy an app from a project
EDIT AN APP (LEGACY)
Edit a tool
Create a workflow
Edit a workflow
Add revision notes
Edit an app
About the editor
The tool editor
About the tool editor
Introduction to tool wrapping
Create a tool
Tool editor tutorial
Input file options
Advanced practices
Dynamic expressions in tool descriptions
Javascript Cookbook
The workflow editor
About the workflow editor
Create a workflow
Workflow editor tutorial
RUN AN ANALYSIS
About analyses
About batch analyses
Run a task
Define app settings
Set computation instances
About secondary (index) files
TASK EXECUTION
About task execution
About controlling task execution
About parallelizing tool executions (Scatter)
About tool resource requirements
About Memoization (Reuse)
Project and file locations (Multi-cloud)
Set execution hints at workflow level
Set execution hints at node level
Set execution hints at tool level
Set execution hints at task level
About Spot Instances
Use Spot Instances
List of execution hints
List of task statuses
List of available Amazon Web Services US instances
List of available Amazon Web Services EU instances
REVIEW A TASK
Review the task page
View task stats
View task logs
Job retry
View instance metrics
Real-time job monitoring
Troubleshoot a failed task
VIEW ANALYSIS RESULTS
View output files
INTERACTIVE ANALYSIS
Interactive analysis on the Platform
Seven Bridges Genome Browser
Variant Browser
VCF Benchmarking app
CummeRbundQC RNA-Seq Visualization
FastQC
Picard Collect Alignment Summary Metrics
The Seven Bridges Coverage app
RHEO
Overview
Manage via CLI
Manage via API
Manage via RHEO visual interface (GUI)
RHEO glossary
RHEO FOR DEVELOPERS
Overview
RHEO Developer tutorial
Installation and configuration
Hello world!
Step inputs
Step nesting, promises, and dependencies
Parallelization and promises
Loops and result gathering
Conditionals
Automating the Seven Bridges Platform
Config files and automation settings
App-executing steps
Singletons and contexts
Type checking
Deploy and run automations on the Seven Bridges Platform
Using the RHEO visual interface (GUI)
Repository structure
Create automations for the RHEO visual interface (GUI)
Automation inputs
Automation outputs
GRAPH GENOME APPS
About Graph Genome apps
Graph WGS
About Graph WGS
Graph Germline Variant Detection Workflow tutorial
DATA STUDIO
About Data Studio
JupyterLab quick reference
RStudio quick reference
Run a Data Studio analysis
Data Studio analysis details
Copy a Data Studio analysis
Data Studio analysis charging
Data Studio analysis editor
Data Studio environments and libraries
DOWNLOAD RESULTS
Download results
DEVELOPER TOOLS
Developer Hub
Get your authentication token
Publish your app in the Public Apps gallery
Integrate your web application
PUBLIC PROJECTS
Public projects overview
Smart Variant Filtering
Data Studio Interactive Analyses
VCF Benchmarking
Cancer Cell Line Encyclopedia (CCLE)
Simons Genome Diversity Project (SGDP) dataset
Human Cell Atlas Preview Datasets
ENTERPRISE FEATURES
About the Enterprise feature
Collaboration within an Enterprise
Manage an Enterprise
Create a Division
Manage Division administrators
Review billing information for all Divisions
Review Enterprise data throughput
Manage a Division
Manage Division members
Manage teams
Review billing information for your Division
Set credit card as payment method
Manage Division notifications
Add a collaborator to an Enterprise project
Switch between Divisions
Manage two-factor authentication
Manage Docker repositories
Single sign-on (SSO) setup
API Hub
API Overview
API tutorials
Introduction to the API tutorial
API Quickstart
API Batch tutorial
API rate limit
Submitting tasks for execution
Copying files between projects
Importing files from a volume
Updating file metadata
Deleting multiple files
Exporting files to a volume
Setting maximum pagination limit in queries
Finding project by name
Using volumes via the API
API CLIENTS
API Clients
Store credentials to access Seven Bridges client applications and libraries
R library
Python library recipes
Python library
Java library
Java library Quickstart
Seven Bridges Command Line Interface
Seven Bridges Command Line Interface Reference
General commands
Billing
Projects and members
Files and metadata
Upload and download files
Apps
Tasks
Volumes
Connect cloud storage
Connect cloud storage overview
Volumes
Aliases
Supported cloud storage providers
Amazon Web Services Simple Storage Service (AWS S3) Volumes
Google Cloud Storage (GCS) Volumes
Security concerns when working with volumes
Enabling cross-origin resource sharing (CORS)
Operations on volumes
About volumes on the visual interface
Attach an Amazon Web Services (AWS) volume
Attach a Google Cloud Storage volume
Manage members for a volume
Browse and add files to a project from a volume
Deactivate a volume
API Cloud storage tutorials
AWS Cloud storage tutorial
Google Cloud Storage tutorial
GLOSSARY
Glossary
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