Workflows

Workflows allow you to execute large-scale bioinformatic pipelines using Nextflow. The platform manages the underlying infrastructure, allowing you to focus on your analysis while providing real-time monitoring and standardized output management.

Launching a New Workflow

To start a computation, click New workflow. The configuration is divided into four main sections:

1. Workflow Definition

Provide the source of your pipeline. You can enter a GitHub repository URL directly or use the Quick start buttons for common pipelines like nf-core/rnaseq or nf-core/sarek. You should specify a Revision (tag, branch, or commit hash) and a unique Run name.

2. Sample Sheet

Select a pre-configured sample sheet to define your input data. Selecting a sample sheet will automatically populate the relevant input parameters in the next section.

User-Uploaded Sample Sheets

If your sample sheet was not created by the Sample Sheets functionality, you need to find the sample sheet parameter for your particular workflow in the parameters list (see next point below) and paste the S3 URI link for the sample sheet you uploaded yourself. Not all workflows may required sample sheets.

3. Parameters

This section allows you to configure pipeline-specific arguments. The platform dynamically renders these based on the workflow's schema; they may include:

• Input/Output: Define where the pipeline finds data. Note that the outdir is managed automatically by the platform.
• Validation: Required parameters are marked with a red asterisk (*). You can toggle between a visual form and a raw JSON editor.

4. Engine Parameters

Configure the execution environment for the Nextflow engine. This includes setting the profile (e.g., k8s, docker), resource limits (max-cpus, max-memory), and enabling the cache or resume functionality.

Denied Parameters

To ensure platform stability and security, certain Nextflow parameters are restricted. These include parameters for reporting, tracing, and specific container engines that are managed natively by the platform. Any denied parameters will be listed at the bottom of the configuration view.

Monitoring and Results

Once you click Review and run, you can verify the final command line before execution. After the run starts, it will appear in the Workflows list.

Run Details

Selecting a run opens the monitoring interface, which consists of four tabs:

• Overview: Displays high-level metadata, including the execution status, duration, and system exit codes.
• Input: Shows the exact command line and configuration used for the run.
• Outputs: Provides a browser to explore the generated data. Output files are managed as DRS (Data Repository Service) bundles for easy referencing in other project assets.
• Logs: Provides a live, streaming view of the execution logs. You can download the full log file or copy segments to your clipboard.

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