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treeval-summary plugin

This project contains a simple Nextflow plugin called treeval-summary to summary metadata and trace of a nextflow run, then store it in a defined DuckDB with 02 tables (meta and trace).

Plugin structure

  • settings.gradle

    Gradle project settings.

  • plugins/treeval-summary

    The plugin implementation base directory.

  • plugins/treeval-summary/build.gradle

    Plugin Gradle build file. Project dependencies should be added here.

  • plugins/treeval-summary/src/resources/META-INF/MANIFEST.MF

    Manifest file defining the plugin attributes e.g. name, version, etc. The attribute Plugin-Class declares the plugin main class. This class should extend the base class nextflow.plugin.BasePlugin e.g. nextflow.summary.SummaryPlugin.

  • plugins/treeval-summary/src/resources/META-INF/extensions.idx

    This file declares one or more extension classes provided by the plugin. Each line should contain the fully qualified name of a Java class that implements the org.pf4j.ExtensionPoint interface (or a sub-interface).

  • plugins/treeval-summary/src/main

    The plugin implementation sources.

Plugin classes

  • SummaryExtension: shows how to create custom function
  • SummaryPlugin: the plugin entry point

Install the plugin

make install

Use plugin in a pipeline

nextflow.config

plugins {
  id 'treeval-summary@0.0.1'
}

workflow

Function summary gather run log data and store that in a DuckDB. This function could be used as:

include { summary } from 'plugin/treeval-summary'

summary( workflow, params, metrics, dbPath)

Where metrics is information related to input data and dbPath is path to existing/desired duckdb to store log data.