Summary

The nf-crg-report plugin provides multiple configurable report types for comprehensive reporting during Nextflow workflow execution:

• 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:

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

    // Report specific options
    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
        format = 'html'
        htmlTemplatePath = 'task-status-report-template.html'
    }

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

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

    // Cost and pricing configuration
    costs {
        priceJsonPath = './prices.json'
        currency = 'EUR'
    }
}

Examples

Basic Configuration

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

    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
    }
}

Sample Status Report with Metadata Extraction

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

When sample_id contains a list (e.g., [sample_id: ['sampleA', 'sampleB']]), the task will be tracked under both sampleA and sampleB.

Cost Estimation Configuration

nfreport {
    costs {
        priceJsonPath = './prices.json'
        defaultGpuMemGb = 16
        currency = 'EUR'
    }

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

Example prices.json:

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

Full Configuration Example

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"
    }
}

License

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