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 and email notifications. The plugin also supports cost estimation for compute and storage resources.

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. Here is a basic configuration example:

nfreport {
    // Global options
    format = 'json'
    outputDir = './reports'
    prefix = 'myworkflow-'
    createLinkToLatestReport = true

    // Report specific options
    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
    }
}

Examples

Basic Configuration

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'
        format = 'html' // Overrides format in nfreport scope
        htmlTemplatePath = 'task-status-report-template.html'
    }

    sampleStatusReport {
        enabled = true
        format = 'html'
    }
}

Sample Status Report with Metadata Extraction

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

Full Configuration with Costs and Email

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

    costs {
        priceAPI = 'https://sit.crg.es/fees'
        defaultGpuMemGb = 16
        currency = 'EUR'
    }

    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

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

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

Pricing JSON Format

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

License

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