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. Here's a basic example:

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

    // Report specific options
    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
    }
}

Examples

Basic Configuration with All Report Types

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

    executionReport {
        enabled = true
        createLinkToLatestReport = false
    }

    taskStatusReport {
        enabled = true
        outputFilename = 'task-status-report'
        format = 'html'
        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'
        printCompletionSummary = true
    }
}

Full Configuration with Cost Estimation and Email Notifications

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"
    }
}

Pricing JSON Example

{
  "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.