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'
}

Then configure the plugin in your nextflow.config file using the nfreport scope:

nfreport {
    outputDir = './reports'
    format = 'json' // or 'html', 'tsv'
    
    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

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

Examples

Basic configuration example:

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'
    }
}

Full configuration with cost tracking 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"
        bcc = "bcc@example.com"
    }
}

Pricing JSON configuration 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.