X-omics ACTIONdemonstrator multi-omics analysis workflow

Here, the ACTIONdemonstrator workflow is made using Nextflow workflow manager. With this workflow, we would like to demonstrate how to create a FAIR workflow. We consider FAIR workflows that follow the FAIR4RS principles by design. This workflows ingests molecular -omics profiling and phenotypic data that is already converted into standardized file formats. This standardization and data-specific pre-processing can be found here in this workflow.

Pipeline summary

The NTR-ACTION analysis workflow consists of a set of different pre-processing and analysis steps:

More complete documentation on the workflow can be found here

WorkflowHub and RO-Crate

The workflow can be found on the WorkflowHub page page as well. Different versions of the workflow will be published here. The webpage provides an option to download the workflow as Research-Object Crate (RO-Crate). This RO-Crate contains all required workflow elements - including metadata describibing these elements - packed into one .zip file. The Jupyter Notebook generate_ro-crate.ipynb demonstrates how the RO-Crate was made.

Requirements

Nextflow and Singularity are required to be installed. To install them on CentOS Linux 7 enable EPEL and run

sudo yum -y install conda.noarch
sudo yum -y install singularity.x86_64

Installing Nextflow

conda create --name nf
conda activate nf
conda install -c bioconda nextflow:22.04.0

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

Usage

Obtain workflow

The workflow RO-Crate can be downloaded from the WorkflowHub page. The RO-Crate contains all necessary files to run the workflow (where this repository does not because of storage limits).

Alternatively, you can clone this git repository (git clone https://github.com/Xomics/ACTIONdemonstrator_workflow.git). Then download the missing Infinium MethylationEPIC product file here, for which a placeholder is located in EPIC_annotation/raw/.

Run main workflow:

For detailed instructions on how to run the workflow:

nextflow run action.nf --help

The typical command to run the workflow is:

nextflow run action.nf 
            --output dir/of/choice
            --mtblmcs_values Sythetic_data/synthetic_metabolomics.csv
            --maf_files Synthetic_data/
            --epigenomics_values Synthetic_data/synthetic_epigenomics.csv
            --epigenomics_meta Synthetic_data/synthetic_epigenomics_meta.csv
            --behavioral_data Synthetic_data/synthetic_cbcl_data.csv
            --phenotype_covariates Synthetic_data/synthetic_phenotype_covariates_data.csv
            --cbcl_labels Synthetic_data/cbcl_labels.csv
            --ids Synthetic_data/ACTIONdemonstrator_XOmics_IDS_synthetic.csv

To run the workflow in the Digital Research Environment:

• Specify config file: -c dre.config
• Specify container files (.sif) dir: --container_dir /dir/to/containers/

Synthetic Data

Synthetic data is provided as example data in Synthetic_data/. This directory contains the necessary (omics) data files to run the workflow + the ISA-Tab files describing the experimental metadata. These ISA files were generated with this repository.

Software containers

Nextflow automatically pulls all necessary Docker containers from Dockerhub, when using the default nextflow.config file. Docker (and Singularity) containers can be built locally as well, see more detailed information in this repository. The dre.config file demonstrates how to allocate local Singularity (.sif) files to Nextflow processes.

Authors

Radboud University Medical Center, Nijmegen, Netherlands:

• Anna Niehues
• Casper de Visser
• Purva Kulkarni
• Alain J. van Gool
• Peter A. C. 't Hoen

Vrije Universiteit Amsterdam, Amsterdam, Netherlands:

• Fiona A. Hagenbeek
• René Pool
• Dorret I. Boomsma
• Jenny van Dongen

Leiden University, Leiden, Netherlands:

• Naama Karu
• Alida S. D. Kindt