X-omics ACTIONdemonstrator analysis workflow

public public 1yr ago Version: Version 2.2 0 bookmarks
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x-omics-actiondemonstrator-analysis-workflow
x-omics-actiondemonstrator-analysis-workflow
x-omics-actiondemonstrator-analysis-workflow
x-omics-actiondemonstrator-analysis-workflow
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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:

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Code Snippets

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"""
cp -L $project_dir/bin/CBCL_filter_impute_MCA.Rmd CBCL_filter_impute_MCA.Rmd
Rscript -e "rmarkdown::render('CBCL_filter_impute_MCA.Rmd', output_format = 'html_document', output_file = 'CBCL_filter_impute_MCA.html', params = list(cbcl_infile = '${pheno}', cbcl_filtered_outfile = 'cbcl_filtered.csv', cbcl_imputed_outfile = 'cbcl_imputed.csv', cbcl_mca_coord_outfile = 'cbcl_mca_coord.csv', cbcl_mca_outfile = 'cbcl_mca.RData', imputation_method = '${params.cbcl_imputation_method}'))"	
"""
NextFlow From line 28 of modules/CBCL_MCA.nf 
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"""
Rscript $project_dir/bin/epigenomics_annotation.R ${epigenomics_MOESM1} ${epigenomics_MOESM4} ${epigenomics_MOESM5} ${MethylationEPIC} ${anno_epic}  'epigenomics_annotation_out.RData'
"""
NextFlow From line 30 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/epigenomics_filtering.R ${epigenomics_values} ${annotation_out}  '${epigenomics_values}_filtered.csv'
"""
NextFlow From line 48 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/epigenomics_imputation.R ${epigenomics_values} 'epigenomics_imputed_${epigenomics_values}.csv'
"""
NextFlow From line 64 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/CovariateCorrection.R ${epigenomics_values}  ${epigenomics_meta} 'epigenomics_corrected.csv'
"""
NextFlow From line 81 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/sort_cols_sd.R ${epigenomics_values} ${feature_cutoff} epigenomics_values_subset.csv
"""
NextFlow From line 97 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/epigenomics_scaling.R ${epigenomics_values} 'epigenomics_scaled.csv'
"""
NextFlow From line 114 of modules/epigenetics_preprocessing.nf 
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"""
Rscript $project_dir/bin/heatmap_missingness.R ${mtblmcs_values} ${epigenomics_values} ${epigenomics_meta} ${behavioral_data} ${phenotype_covariates} heatmap_missingness.pdf
"""
NextFlow From line 31 of modules/heatmap_missingness.nf 
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"""
python3 $project_dir/bin/map_IDs.py ${epigenomics_values} ${mtblmcs_values} ${ids} epigenomics_values_mapped.csv metabolomics_values_mapped.csv duplicates_discarded.csv
"""
NextFlow From line 25 of modules/map_IDs.nf 
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"""
cp -L $project_dir/bin/metabolomics_filter.Rmd metabolomics_filter.Rmd
Rscript -e "rmarkdown::render('metabolomics_filter.Rmd', output_format = 'html_document', output_file = 'metabolomics_filter.html',  params = list(MAF_path = '${MAF}', output_dir_csv = '${MAF}_filtered.csv', missing_value_cutoff = '${missingness_cutoff}'  ))"
"""
NextFlow From line 20 of modules/metabolomics_preprocessing.nf 
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"""
Rscript $project_dir/bin/metabolomics_normalization.R ${mtblmcs_filtered} ${mtblmcs_values} ${mtblmcs_filtered}_normalized.csv ${normalization_type}
"""
NextFlow From line 39 of modules/metabolomics_preprocessing.nf 
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"""
Rscript $project_dir/bin/metabolomics_scaling.R  ${mtblmcs_values} ${mtblmcs_values}_scaled.csv 
"""
NextFlow From line 55 of modules/metabolomics_preprocessing.nf 
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"""
Rscript $project_dir/bin/concatenate_MAF.R ${mtblmcs_files} metabolomics_preprocessed.csv
"""
NextFlow From line 71 of modules/metabolomics_preprocessing.nf 
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"""
Rscript $project_dir/bin/pca.R ${mtblmcs_values} ${epigenomics_values} ${epigenomics_meta} ${phenotypes_set2} ${ids} pca.pdf
"""
NextFlow From line 30 of modules/pca.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/Xomics/ACTIONdemonstrator_workflow
Name: x-omics-actiondemonstrator-analysis-workflow
Version: Version 2.2
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