Bioinformatics & Computational Biology | Molecular Genetics
Senior Bioinformatician @ UMass Medical School | haibo.liu@umassmed.edu
Overview
Introduction
Introduction
This guide provides essential Groovy syntax and examples specifically tailored for building sophisticated Nextflow pipelines. It focuses on the most commonly used Groovy features in Nextflow workflows.
Introduction
This document outlines best practices for creating and managing Nextflow configuration files, including nextflow_schema.json, modules.json, nextflow.config, HPC cluster configurations, AWS Batch configurations, parameter files, and testing strategies.
This document outlines best practices for writing the main workflow file (main.nf) for Nextflow pipelines. This is the entry point that users run and orchestrates all modules and subworkflows.
This document outlines best practices for creating Nextflow subworkflows that combine multiple modules into reusable, composable workflow units.
This document outlines best practices for writing comprehensive nf-test test files for Nextflow modules, covering test structure, patterns, assertions, and configuration.
This document outlines best practices for organizing and writing conf/modules.config files for Nextflow pipelines with many modules and complex conditional execution logic.
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