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 task execution and email notifications.

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. Here's a basic example to enable all three report types:

nfreport {
    outputDir = './reports'
    format = 'json'
    
    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
    }
}

To test the plugin without a local Nextflow installation:

1. Build and install: make install
2. Run a pipeline: nextflow run hello -plugins nf-crg-report@1.1.4

Examples

Basic Configuration with All Reports

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

    executionReport {
        enabled = true
    }

    taskStatusReport {
        enabled = true
    }

    sampleStatusReport {
        enabled = true
    }
}

Advanced Configuration with HTML Reports and Cost Tracking

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

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

    executionReport {
        enabled = true
    }

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

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

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

Sample Name Extraction from Metadata Map

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

Pricing Configuration with JSON File

{
  "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.