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nextflow.config
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manifest {
name = 'nf-gwas'
version = '1.0.0'
description = 'A Nextflow GWAS pipeline.'
author = 'Lukas Forer and Sebastian Schönherr'
homePage = 'https://github.com/genepi/nf-gwas'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
}
// Global default params, used in configs
params {
//Required inputs
project = null
genotypes_array = null
genotypes_imputed = null
genotypes_build = null
association_build = null
target_build = null
genotypes_imputed_format = null
phenotypes_filename = null
phenotypes_columns = null
phenotypes_binary_trait = false
regenie_test = null
genotypes_association = null
genotypes_association_format = null
genotypes_association_chunk_size = 0
genotypes_association_chunk_strategy = 'RANGE'
genotypes_prediction = null
genotypes_prediction_chunks = 0
//Optional inputs
outdir = null
project_date = "`date`"
covariates_filename = null
covariates_columns = null
covariates_cat_columns = null
phenotypes_delete_missings = false
phenotypes_apply_rint = false
rsids_filename = null
//Interaction test options
regenie_interaction = null
regenie_interaction_snp = null
regenie_rare_mac = 1000
regenie_no_condtl = false
regenie_force_condtl = false
//gene-based tests options
regenie_run_gene_based_tests = false
regenie_run_interaction_tests = false
regenie_gene_masks = null
regenie_gene_setlist = null
regenie_gene_anno = null
regenie_gene_aaf = null
regenie_gene_test = null
regenie_gene_joint = null
regenie_gene_build_mask = null
regenie_write_bed_masks = false
regenie_gene_vc_mac_thr = null
regenie_gene_vc_max_aaf = null
//Conditional analyses
regenie_condition_list = null
//SNP_PRUNING process
prune_enabled = false
prune_maf = 0.01
prune_window_kbsize = 1000
prune_step_size = 100
prune_r2_threshold = 0.9
//QC_FILTER process
qc_maf = 0.01
qc_mac = 100
qc_geno = 0.1
qc_hwe = '1e-15'
qc_mind = 0.1
// VCF IMPUTED TO PLINK2
vcf_conversion_split_id = false
//REGENIE_STEP1 + REGENIE_STEP_2 process
regenie_bsize_step1 = 1000
regenie_bsize_step2 = 400
regenie_sample_file = null
regenie_skip_predictions = false
regenie_min_imputation_score = 0.00
regenie_min_mac = 5
regenie_range = null
regenie_firth = true
regenie_firth_approx = true
regenie_force_step1 = false
regenie_ref_first = false
regenie_low_mem = true
//Annottion and Manhattan Plot
annotation_min_log10p = 7.3
annotation_peak_pval = 1.5
annotation_max_genes = 20
//REPORT process
plot_ylimit = 0
manhattan_annotation_enabled = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
process.container = 'quay.io/genepi/nf-gwas:v1.0.0'
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
test {
includeConfig 'conf/test.config'
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
}
development {
process.container = 'genepi/nf-gwas:latest'
docker.enabled = true
docker.userEmulation = true
resume = true
singularity.enabled = false
}
slurm {
process.executor = 'slurm'
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
maxErrors = '-1'
maxRetries = 3
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
}
slurm_with_scratch {
process.executor = 'slurm'
process.scratch = true
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
maxErrors = '-1'
maxRetries = 3
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
}
}