N4M Results Summry

Nextflow pipeline for summarizing results obtained from other data processing workflows in Nextflow4Metabolomics Suite.

Introduction

N4M Results Summry is a workflow that summarize LC-HRMS metabolomics data processing results obtained from other workflows in the Nextflow4Metabolomics Suite.

• The pipeline containers two processes: 1) merging peaks from two peak tables, the two peak tables can be obtained by runnin the same workflow using two OS; 2) quantifiying peaks before and after merging.

• The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

• The workflow support MacOS and Linux operating systems.

Installation

1. Install nextflow

2. Install Docker or Singularity for full pipeline reproducibility.

Quick Start

1. Download the pipeline repo and dirct to the folder:

   git clone https://github.com/Nextflow4Metabolomics/n4m_results_summary.git && cd n4m_results_summary

2. Run the pipeline with example data:

   nextflow main.nf -profile functional_test > logs/execution.log

Process Your Own Data

1. Put the data files in the folder data/, and named the two files table_1 and table_2, note that table_2 should have less peaks than table_1.
2. Run the pipeline (use "docker" as the profile when running locally, and "singularity" as the profile when running with a high-performance computing system):

   nextflow main.nf -profile docker > logs/execution.log

Configuration

• Configuration for running with Docker are set in the file conf/base.config.
• Configuration for running with High-Performance Computing and Singularity are set in the file conf/HiPerGator.config.
• Parameters for MS-DIAL and MS-FLO are set in their specific configuration files.

Credits

Dr. Dominick Lemas (Xinsong Du's Ph.D. advisor) and Xinsong Du play an important role on conceptulization. The nextflow4ms-dial was mainly developed by Xinsong Du.

We thank the following people for their extensive assistance in the development of this pipeline: