EATRIS-Plus Multi-omics Analysis Workflow

Analysis workflow used to analyze the cohort of healthy blood donors

Prerequisites

Multi-omics data set from Zenodo

• The data is stored in a Multi_Assay_Experiment object, which is used as input for the workflow
• The object can be downloaded here: https://doi.org/10.5281/zenodo.10782799

Install Nextflow using conda

Create a Conda Environment:

   conda create -n nextflow-env
   conda activate nextflow-env
   conda install -c bioconda nextflow

See also https://anaconda.org/bioconda/nextflow and https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html.

Singularity

For detailed Singularity installation instructions, please refer to the official Singularity installation guide.

Software containers

All software containers used in this workflow can be obtained here

Execute Analysis Workflow

For more instructions on how to run the workflow:

nextflow run main.nf --help

The typical command to run the workflow is:

nextflow run main.nf 
 	-c dre.config 
	--config_file config.yml
	--references references.bib 
	--mae_object /dir/MAE_object
	--container_dir /dir/containers/
	--output dir/of/choice

Run time

This workflow was tested on a Linux environment with 16 CPU cores and 32 GB RAM available. For this hardware, the run times recorded for the individual Nextflow processes are documented here