The Convergence of Science and Technology
Science and technology have evolved together over the last 25 years. We've witnessed transformative scientific breakthroughs from the Human Genome Project and NGS through CRISPR gene editing and AlphaFold. Meanwhile technology exploded from basic computing to powerful cloud platforms and AI. These aren't separate stories; they're completely intertwined. Scientific discoveries these days are impossible without sophisticated technology and computing power.
As science accelerated, teams needed more than just workflow tools, they needed better data integration, scalability, and collaboration. Scientific progress was getting stuck because the technology was too complex. That’s why we created Nextflow and Seqera. In this blog post, we highlight six core problems that make bioinformatics harder than it should be and how Seqera, the Nextflow-first tech stack, addresses each one.
6 Reasons Why Bioinformatics is Hard
1. Orchestrating Complex Multi-Step Analyses
The Problem
Your typical bioinformatics workflow isn't a single script, it’s multiple interconnected steps, each requiring different tools, parameters, and resources. The manual approach to managing this becomes a tedious cycle of running steps sequentially, waiting for completion, debugging failures, managing file transfers, and repeating the entire process for every sample, turning data analysis into manual project management that doesn't scale.
How Seqera Helps
Nextflow transforms this chaos into reproducible workflows. Write your pipeline once, and it handles automatic dependency management between steps, parallel execution, failure handling and automatic retries, progress tracking across all samples, and execution on any compute environment. Seqera AI, the bioinformatics agent built for Nextflow, makes generating and debugging workflows even easier, helping you translate your analysis logic into robust Nextflow code.
💡Hint: With the Seqera AI Copilot VS Code extension, you can generate, edit, and troubleshoot DSL2-compliant Nextflow code using natural language directly in your IDE.
2. Ensuring Reproducibility
The Problem
Nextflow pipelines often require multiple different software tools, each with specific version dependencies. For example, nf-core/ampliseq requires 15 different software tools to work. Getting these tools to work together consistently across different environments (your laptop, the HPC cluster, the cloud) is like solving a puzzle where the pieces keep changing shape. One missing dependency or version mismatch can break everything.
How Seqera Helps
Wave eliminates dependency hell by automatically building containers for your analysis tools on demand and during pipeline execution. Just specify your software requirements and Wave handles the rest. It creates a container with everything preconfigured to work together, anywhere. Seqera Containers complements Wave with a user-friendly web interface that lets you build, browse, and manage containers on the fly without CLI, making container management accessible to everyone.
💡Hint: Wave offers a suite of features designed to simplify the configuration, provisioning, and management of software containers for data pipelines at scale. Wave can be enabled in your Nextflow pipeline in Seqera Platform.
3. Accessing the Data
The Problem
While the cloud promises unlimited compute power and pay-as-you-go scaling, the reality involves navigating IAM roles, permissions, VPCs, S3 buckets, and surprise bills. Traditional approaches require downloading terabytes or writing complex data staging scripts, creating bottlenecks that slow down your entire analysis. What should be straightforward data access becomes a complex infrastructure challenge.
How Seqera Helps
Fusion, the cloud-native file system optimized for Nextflow, makes large cloud datasets appear as local files to your analysis tools, allowing you to bring compute to the data. Data Explorer provides a unified interface to browse and manage data wherever it lives (across cloud storage buckets, providers, regions, or on-prem systems) directly from Seqera Platform, with seamless integration into pipeline launches and run monitoring.
💡Hint: Fusion simplifies infrastructure, enhances pipeline performance and cuts costs, making it easier to develop, maintain, and scale pipeline code. Fusion can be enabled in your Nextflow pipeline in Seqera Platform.
4. Compute Resources
The Problem
Nextflow pipelines often need more compute power than your local resources can provide. But, setting up cloud computing often means configuring AWS Batch queues, auto-scaling groups, and IAM permissions. This forces bioinformaticians into an unwelcome choice: accept compute limitations or divert research time to mastering cloud infrastructure.
How Seqera Helps
Seqera Platform gets you running in the cloud within minutes. Batch Forge automatically creates and configures cloud environments for instant use. For even simpler access, Seqera Compute lets you buy credits and start computing with two clicks. No cloud expertise required, no surprise bills, no setup, just straightforward access to scalable compute resources.
💡Hint: Batch Forge automates the configuration of compute environments in Seqera Platform, provisioning everything needed to deploy pipelines at scale (queues, permissions, networking, and storage), eliminating the need for custom AMIs or complex templates.
5. Understanding Results
The Problem
Nextflow pipelines can generate results across multiple file formats (e.g. text files, plots, images, and log files) distributed throughout output directories. Each file contains important information, but extracting insights from disparate outputs becomes a time-consuming manual process that delays interpretation and reduces analytical efficiency.
How Seqera Helps
MultiQC automatically aggregates and processes scattered result files from your pipeline, generating comprehensive, interactive reports with standardized visualizations. Studios provides cloud-based interactive analysis environments for deeper result exploration, seamlessly integrating your existing Seqera compute and data infrastructure. This enables immediate post-pipeline analysis without additional setup or data transfer.
💡Hint: Studios is the interactive analysis feature of Seqera Platform which allows you to bring reproducible and containerized analytical environments to your data in real-time.
6. Real-Time Collaboration
The Problem
Sharing analyses and results is often difficult. Pipeline parameters, compute environment configurations, software container versions, and distributed datasets may be scattered across local setups or storage systems. This makes standardization and reproducibility difficult. What should be straightforward scientific collaboration becomes a time-consuming exercise in reverse engineering your computational setup.
How Seqera Helps
Seqera Platform centralizes all analysis components for seamless sharing and reproducibility. Launch and configure pipelines, monitor real-time progress with cost and resource tracking, and maintain complete audit trails of every parameter, dataset, and environment component. Teams can share entire analysis configurations enabling colleagues to reproduce workflows exactly as originally executed. Studios also enables real-time collaborative analysis sessions where multiple team members can simultaneously work within the same interactive environment.
Seqera: The Platform Optimized for Nextflow
We understand that bioinformatics is hard enough without fighting your tools. Built by bioinformaticians for bioinformatics, Seqera was developed and optimized for Nextflow from day one. Our software-first approach treats containers, git, and code as first-class citizens, supporting your full pipeline development lifecycle, from data through to results. Scale your existing Nextflow workflows with integrated tools designed around how you already work.
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