nextflow.config

docker {
	enabled = true
	userEmulation = true
}


params {

	// Filtering
	missingness_cutoff = 0.15

	// Normalization
	mtblmcs_normalization_type = 'cr'

	// Imputation
	cbcl_imputation_method = "RF"

	// Scaling
	scale_epigenomics = false

	// Features subsets
	feature_subset_cutoff = 10

	// MOFA parameters
	seed = 100
	convergence_mode = "slow" 


	// Input files parameters
	epigenomics_values = null
	epigenomics_meta = null
	mtblmcs_values = null
	maf_files = null
	ids = null
	phenotype_covariates = null
	behavioral_data = null	
	cbcl_labels = null
	gee	= null

	output = null
}


r_base_analysis = "casperdevisser/r-base-analysis:v0.4"
epigenomics_preprocessing = "casperdevisser/r-base-epigenomics-pre:v0.4"
phenotypes_preprocessing = "casperdevisser/r-base-phenotypes:v0.6"
snf = "casperdevisser/miniconda-snf:v0.7"
mofa = "casperdevisser/mofa2:v0.6"

process {

  // Assign containers to single processes 
	withName:METABOLOMICS_FILTERING {
		container = "$phenotypes_preprocessing"
	}
	withName:EPIGENOMICS_ANNOTATION {
		container = "$epigenomics_preprocessing"
	}
	withName:EPIGENOMICS_FILTERING {
		container = "$r_base_analysis"
	}
	withName:EPIGENOMICS_IMPUTATION {
		container = "$r_base_analysis"
	}
	withName:EPIGENOMICS_COVARIATES {
		container = "$r_base_analysis"
	}
	withName:EPIGENOMICS_SCALING {
		container = "$r_base_analysis"
	}
	withName:CBCL_FILTER_IMPUTE_MCA {
		container = "$phenotypes_preprocessing"
	}
	withName:PCA {
		container = "$r_base_analysis"
	}
	withName:SUBSET_SD {
		container = "$r_base_analysis"
	}
	withName:SNF {
		container = "$snf"
	}
	withName:SNF_ANALYSIS {
		container = "$snf"
	}
	withName:SNF_GEE {
		container = "$mofa"
	}
	withName:MAP_IDS {
		container = "$snf"
	}
	withName:MOFA {
		container = "$mofa" 
	}
	withName:MOFA_ANALYSIS {
		container = "$mofa" 
	}
	withName:MOFA_ANALYSIS_WITH_GEE {
		container = "$mofa"
	}
	// Assign containers to multiple processes sharing a label
	withLabel: r_base_analysis_small_tasks {
	  container = "$r_base_analysis"
	}
	
	
	/* 
	Max resources of the computational environment should be specified here:
	*/
	withLabel: full_resources {
		cpus = 4
		memory = 15.GB
	}
}


def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.output}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.output}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.output}/execution_trace_${trace_timestamp}.txt"
	fields = 'task_id,name,process,status,exit,realtime,%cpu,cpus,container,rss'
}
dag {
    enabled = true
    file    = "${params.output}/pipeline_dag_${trace_timestamp}.html"
}


manifest {
    name            = 'Xomics/ACTIONdemonstrator_workflow'
    author          = 'Anna Niehues, Casper de Visser, Fiona Hagenbeek, Naama Karu, Alida Kindt, Purva Kulkarni, Rene Pool, Dorret Boomsma, Jenny van Dongen, Alain van Gool, Peter-Bram t Hoen'
    homePage        = 'https://github.com/Xomics/ACTIONdemonstrator_workflow'
    description     = 'Reproducible workflow for multi-omics behavioral data'
    mainScript      = 'action.nf'
    nextflowVersion = '!>=22.04.0'
    version         = '1.1'
}