# 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:** ```bash 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](https://docs.sylabs.io/guides/3.0/user-guide/installation.html). ### Software containers All software containers used in this workflow [can be obtained here](https://github.com/Xomics/Docker_containers) # 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](/RunTest/execution_trace_2025-12-05.txt)