Seqera vs. Nextflow

vs.

A comprehensive feature comparison between Seqera Platform and Nextflow. Discover what you can do with Nextflow, and understand what additional features Seqera provides.

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Unlock the full potential of Nextflow with Seqera

Seqera is the Nextflow-first platform for scalable bioinformatics, bringing together data, compute, pipelines, and interactive analysis.

Built by the creators of Nextflow, Seqera delivers a seamless journey from development to production with enterprise-ready visibility at every level.

Pipeline Execution
Launch methods	Web based launchpad with forms CLI for power users API to build your own integrations Event-based pipeline actions	CLI - requires manual parameter specification
Workflow monitoring	Real-time workflow monitoring via web UI, CLI, API Comprehensive dashboard Centralized run information, even across diverse compute systems Event-based pipeline actions Workflow execution metadata	Basic execution tracking

Pipeline Execution

Launch methods

Web based launchpad with forms
CLI for power users
API to build your own integrations
Event-based pipeline actions

CLI - requires manual parameter specification

Workflow monitoring

Real-time workflow monitoring via web UI, CLI, API
Comprehensive dashboard
Centralized run information, even across diverse compute systems
Event-based pipeline actions
Workflow execution metadata

Basic execution tracking

Collaboration
Team coordination	Git-based code sharing Multi-user workspaces and organizations Shared pipelines, datasets, and compute environments	Git-based code sharing, single-user focus
Access control	Granular permissions with admin, maintainer, participant roles across workspaces	No built-in access controls, system-level
Credential management	Centralized workspace credentials with secure sharing	Manual credential handling per user
Storage integration	Cloud storage integrations Fusion for optimized data movement and cost reduction Fusion snapshots for seamless spot instance recovery	Manual data integration and management

Collaboration

Team coordination

Git-based code sharing
Multi-user workspaces and organizations
Shared pipelines, datasets, and compute environments

Git-based code sharing, single-user focus

Access control

Granular permissions with admin, maintainer, participant roles across workspaces

No built-in access controls, system-level

Credential management

Centralized workspace credentials with secure sharing

Manual credential handling per user

Storage integration

Cloud storage integrations
Fusion for optimized data movement and cost reduction
Fusion snapshots for seamless spot instance recovery

Manual data integration and management

Data Management
Cross-cloud access	Mount object storage from any cloud provider transparently	Limited to local or explicitly configured storage
Data access and organization	Data Explorer for browsing, organizing and sharing data Workspace-managed Datasets for simplified pipeline inputs and centralized data links Metadata curation	Manual file system navigation, separate tools needed
Storage integration	Cloud storage integrations Fusion for optimized data movement and cost reduction Metadata curation Fusion snapshots for seamless spot instance recovery	Manual data integration and management

Data Management

Cross-cloud access

Mount object storage from any cloud provider transparently

Limited to local or explicitly configured storage

Data access and organization

Data Explorer for browsing, organizing and sharing data
Workspace-managed Datasets for simplified pipeline inputs and centralized data links
Metadata curation

Manual file system navigation, separate tools needed

Storage integration

Cloud storage integrations
Fusion for optimized data movement and cost reduction
Metadata curation
Fusion snapshots for seamless spot instance recovery

Manual data integration and management

Compute Infrastructure
Environment setup	One-click Batch Forge deployment compute environments Fully managed Seqera Compute Streamlined AWS and GCP compute environments for faster, simpler compute instance management	Manual integration, configuration for multiple compute environments
Resource management	ML-driven resource recommendations Automated cloud resource provisioning Usage monitoring dashboards	Manual performance tuning and resource allocation
Cost optimization	Cost savings with Fusion and Pipeline Optimization	No built-in optimization

Compute Infrastructure

Environment setup

One-click Batch Forge deployment compute environments
Fully managed Seqera Compute
Streamlined AWS and GCP compute environments for faster, simpler compute instance management

Manual integration, configuration for multiple compute environments

Resource management

ML-driven resource recommendations
Automated cloud resource provisioning
Usage monitoring dashboards

Manual performance tuning and resource allocation

Cost optimization

Cost savings with Fusion and Pipeline Optimization

No built-in optimization

Pipeline Development
Develop reproducible data pipelines	Gold standard for bioinformatics with world-class IDE support Develop pipeline code directly in your compute environment with Studios	Gold standard for bioinformatics with world-class IDE support
Pipeline debugging	Full access to logs and metrics Web-based visualization dashboards In-platform debugging with Studios VS Code in the browser Troubleshoot pipelines using natural language with Seqera AI	Manual investigation across systems
Container support	Advanced container support via Wave Seqera Containers: Free on-demand containers for any combination of Bioconda packages Web UI to inspect container details and build logs	Advanced container support via Wave Seqera Containers: Free on-demand containers for any combination of Bioconda packages

Pipeline Development

Develop reproducible data pipelines

Gold standard for bioinformatics with world-class IDE support
Develop pipeline code directly in your compute environment with Studios

Gold standard for bioinformatics with world-class IDE support

Pipeline debugging

Full access to logs and metrics
Web-based visualization dashboards
In-platform debugging with Studios VS Code in the browser
Troubleshoot pipelines using natural language with Seqera AI

Manual investigation across systems

Container support

Advanced container support via Wave
Seqera Containers: Free on-demand containers for any combination of Bioconda packages
Web UI to inspect container details and build logs

Advanced container support via Wave
Seqera Containers: Free on-demand containers for any combination of Bioconda packages

Reproducibility and Traceability
Workflow tracking	Comprehensive workflow tracking, logging, provenance and history with full audit trails Workflow execution metadata GxP-aligned auditing	Basic execution logging and task isolation
Environment consistency	Container support Encapsulated workflows, inputs and compute environments	Container support for consistent environments

Reproducibility and Traceability

Workflow tracking

Comprehensive workflow tracking, logging, provenance and history with full audit trails
Workflow execution metadata
GxP-aligned auditing

Basic execution logging and task isolation

Environment consistency

Container support
Encapsulated workflows, inputs and compute environments

Container support for consistent environments

Analytics and Reporting
Visualization and metrics	Interactive dashboards Advanced visualization tools Comprehensive reporting	Basic HTML reports
Post-pipeline analysis	Spin-up pre-built reproducible interactive environments in Studios Bring your own custom tools and applications to the data	Manual environment management, fragmented processes

Analytics and Reporting

Visualization and metrics

Interactive dashboards
Advanced visualization tools
Comprehensive reporting

Basic HTML reports

Post-pipeline analysis

Spin-up pre-built reproducible interactive environments in Studios
Bring your own custom tools and applications to the data

Manual environment management, fragmented processes

Automation
Pipeline orchestration	API, CLI, SDK automation Event-based pipeline actions	Basic pipeline execution
AI assistance	Seqera AI for debugging, best practices, code generation, and pipeline building	No built-in development assistance

Automation

Pipeline orchestration

API, CLI, SDK automation
Event-based pipeline actions

Basic pipeline execution

AI assistance

Seqera AI for debugging, best practices, code generation, and pipeline building

No built-in development assistance

Support
Community resources	Curated community pipelines Ability to import with single click	Curated community pipelines
Professional assistance	Dedicated expert support team Professional services and training from Nextflow creators	Community support only (Slack + forum) Self-serve online training materials

Support

Community resources

Curated community pipelines
Ability to import with single click

Curated community pipelines

Professional assistance

Dedicated expert support team
Professional services and training from Nextflow creators

Community support only (Slack + forum)
Self-serve online training materials

Nextflow powers the science. Seqera powers the organization.

24%

reduction in time-to-results

10x

genomic surveillance capacity

50%

reduction in runtime

Ready to get started with Seqera?

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