Summary

The nf-crg-report plugin provides multiple configurable report types for Nextflow workflows:

• Execution Report: Provides a detailed overview of the workflow execution, including start/end times, parameters, and metadata.
• Task Status Report: Summarizes task execution details grouped by status (e.g., COMPLETED, FAILED, CACHED, RETRIED, ABORTED, IGNORED).
• Sample Status Report: Tracks sample processing across the workflow, with samples grouped by their processing status.

The reports can be generated in JSON, HTML, and TSV formats, with customizable templates for HTML reports. The plugin also supports cost estimation for tasks and email notifications.

Get Started

Add the plugin to your Nextflow configuration:

plugins {
    id 'nf-crg-report'
}

Configure the plugin in your nextflow.config file using the nfreport scope. Below is an example configuration demonstrating how to specify global options and report-specific options:

nfreport {
    // Global options
    format = 'json' // or 'html'
    outputDir = './reports'
    prefix = 'myworkflow-'
    suffix = "-${new Date().format('yyyyMMdd')}"
    createLinkToLatestReport = true

    // Report specific options
    executionReport {
        enabled = true
        createLinkToLatestReport = false // Override global setting
    }

    taskStatusReport {
        enabled = true
        outputFilename = 'task-status-report' // Specify custom output filename
        format = 'html' // Overrides format in nfreport scope
        htmlTemplatePath = 'task-status-report-template.html' // Use custom HTML template to render report
    }

    sampleStatusReport {
        enabled = true
        format = 'html' // Overrides format in nfreport scope
    }
}

Examples

Basic Configuration

nfreport {
    outputDir = './reports'
    prefix = 'myworkflow-'
    createLinkToLatestReport = true

    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
        extractSampleNameFrom = 'meta_map'
        sampleNameMetaKeyPattern = 'sample_id'
    }
}

Full Configuration with Cost and Email

nfreport {
    outputDir = './reports'
    prefix = 'myworkflow-'
    createLinkToLatestReport = true

    // Cost and pricing configuration
    costs {
        priceAPI = 'https://sit.crg.es/fees' // Alternative: priceJsonPath = './prices.json'
        defaultGpuMemGb = 16
        currency = 'EUR'
    }

    // Execution report configuration
    executionReport {
        enabled = true
    }

    // Task status JSON report
    taskStatusReport {
        enabled = true
    }

    // Sample status JSON report
    sampleStatusReport {
        enabled = true
        extractSampleNameFrom = 'meta_map'
        sampleNameMetaKeyPattern = 'sample_id'
    }

    // Email notifications
    email {
        enabled = true
        subject = "Workflow Report"
        to = "user@example.com"
        cc = "cc@example.com"
        bcc = "bcc@example.com"
    }
}

Pricing JSON Example

{
  "currency": "EUR",
  "kCPUHr": 9.69,
  "kGBHr": 1.08,
  "kGPUGBHr": 11.63,
  "TBMonth": 3.3
}

Testing the Plugin

make assemble
make install
nextflow run hello -plugins nf-crg-report@1.1.1

License

This project is licensed under the Apache License, Version 2.0. See the COPYING file for details.