Data preparation workflow

This workflow converts the original data of ACTION-NTR and CURIUM that was uploaded to the Digital Research Environment (DRE) into standardized formats, through which they can be used as input for the main workflow.

Pipeline summary

The NTR-ACTION data preparation workflow consists of a set of different steps:

Documentation

More complete documentation on the workflow can be found here

Usage

Run main workflow:

For detailed instructions on how to run the workflow:

nextflow run action_file_preparation.nf  --help

To run the workflow with the NTR-ACTION cohort:

nextflow run action_file_preparation.nf 
	--output  /dir/of/choice
	--container_dir /mnt/workspace/Singularity/ 
	--mtblmcs_values /mnt/workspace/Data/metabolomics_and_biomarkers/upload/XOmics_NTR_ACTION_MtblmcsValues.tsv 
	--mtblmcs_variables /mnt/workspace/Data/metabolomics_and_biomarkers/upload/XOmics_NTR_ACTION_MtblmcsVariables.tsv 
	--mtblmcs_dictionary /mnt/workspace/Data/metabolomics_and_biomarkers/upload/ACTION_dictionary.xlsx 
	--phenotypes_set2 /mnt/workspace/Data/phenotypes/upload/NTR_2056_Jenny_van_Dongen_ActionDemonstrator_set2_20210202.sav 
	--phenotypes_set3 /mnt/workspace/Data/phenotypes/upload/NTR_2056_Jenny_van_Dongen_ActionDemonstrator_set3_20210202.sav 
	--epigenomics_values /mnt/workspace/Data/epigenetics/Drake_input_files/ACTION.EPIC.betas_NTR.csv
	--epigenomics_meta /mnt/workspace/Data/epigenetics/upload/ACTION.metadata_NTR_22092020.RData 
	--ids /mnt/workspace/Data/IDs/ACTIONdemonstrator_XOmics_IDs_09022021.csv 
	--T_scores /mnt/workspace/Data/phenotypes/upload/TR_2714_Action_Tscores_ASEBA_20210628.sav

To run the workflow with the CURIUM cohort:

nextflow run action_file_preparation.nf 
	--output  /dir/of/choice
	--container_dir /mnt/workspace/Singularity/ 
	--mtblmcs_values /mnt/workspace/Data/CURIUM/20220429_PreQC_ValuesDF_CuriumXomics.csv 
	--mtblmcs_variables  /mnt/workspace/Data/CURIUM/20220429_PreQC_VariableDF.csv--mtblmcs_variables
	--mtblmcs_sample_meta /mnt/workspace/Data/CURIUM/20220429_CuriumVariablesForMtblmcsQC_CuriumXomics.csv
	--mtblmcs_dictionary /mnt/workspace/Data/metabolomics_and_biomarkers/upload/ACTION_dictionary.xlsx #Same as for ACTION-NTR
	--phenotypes_set2 /mnt/workspace/Data/CURIUM/ACTION_clinical_CuriumXomics.csv
	--epigenomics_values /mnt/workspace/Data/CURIUM/ACTION.EPIC.betas_curium.csv
	--epigenomics_meta /mnt/workspace/Data/CURIUM/ACTION.metadata_Curium_23082022.Rdata
	--ids /mnt/workspace/Data/CURIUM/ACTIONdemonstrator_Curium_XOmics_IDs_09062022.csv 
	--curium

Using containers

Create Docker image, convert to Singularity

Define a Dockerfile (example: Container_files\r-base-phenotypes\Dockerfile), build Docker image, push to registry, save to archive, and convert to Singularity image.

Build docker image on a local machine and push to the registry:

docker login registry.cmbi.umcn.nl
docker build -t registry.cmbi.umcn.nl/x-omics-action-dataset/action_nextflow/r-base-phenotypes:$VERSION .
docker push registry.cmbi.umcn.nl/x-omics-action-dataset/action_nextflow/r-base-phenotypes:$VERSION

Run in the Digital Research Environment:

docker pull registry.cmbi.umcn.nl/x-omics-action-dataset/action_nextflow/r-base-phenotypes:$VERSION
docker images # to get IMAGE_ID
docker save $IMAGE_ID -o r-base-phenotypes.tar
sudo singularity build r-base-phenotypes.sif docker-archive://r-base-phenotypes.tar