Optional Parameters


Option Default Description
outdir “output/${params.project}” Output directory
project_date today Date in report
covariates_filename empty path to covariates file
covariates_columns empty List of covariates
covariates_cat_columns empty List of categorical covariates
phenotypes_delete_missings false Removing samples with missing data at any of the phenotypes
phenotypes_apply_rint false Apply Rank Inverse Normal Transformation (RINT) to quantitative phenotypes in both steps
target_build empty Specify the desired target_build (hg19 or hg38) of your data. In case it’S different from the input data, lift-over is executed


nf-gwas allows to split your prediction and association data in smaller chunks to utilize large-scale clusters.

Option Default Description
genotypes_association_chunk_size 0 Desired chunksize in bases. if 0, split by chromosomes in regenie_step2
genotypes_association_chunk_strategy ‘RANGE’ Chunking strategy by range or by variants (RANGE or VARIANTS)
genotypes_prediction_chunks 0 Chunking for regenie_step 1. If 0, no chunking of predictions

Annotation and GWAS Report

For annotation, a rsid file is required. If not set, this will be downloaded each time. You can also prepare the file once and set it in your pipeline. Substitute rsbuild with hg19 or hg38.

wget https://resources.pheweb.org/rsids-v154-${rsbuild}.tsv.gz -O rsids-v154-${rsbuild}.tsv.gz
echo -e "CHROM\tPOS\tRSID\tREF\tALT" | bgzip -c > rsids-v154-${rsbuild}.index.gz
zcat rsids-v154-${rsbuild}.tsv.gz | bgzip -c >> rsids-v154-${rsbuild}.index.gz
tabix -s1 -b2 -e2 -S1 rsids-v154-${rsbuild}.index.gz
Option Default Description
rsids_filename empty rsID file for annotation (see above)
annotation_min_log10p 7.3 Annotation limit for interactive and static report
annotation_peak_pval 1.5  
annotation_max_genes 20 Number of max annotated genes

Static Report

Option Default Description
plot_ylimit 0 Limit y axis in Manhattan/QQ plot for large p-values
manhattan_annotation_enabled true Use annotation for Manhattan plot

Pruning Step

Option Default Description
prune_enabled false Enable pruning step
prune_maf 0.01 MAF filter
prune_window_kbsize 1000 Window size
prune_step_size 100 Step size (variant ct)
prune_r2_threshold 0.9 Unphased hardcall R2 threshold

Quality Control (QC) of Predictions

Option Default Description
qc_maf 0.01 Minor allele frequency (MAF) filter
qc_mac 100 Minor allele count (MAC) filter
qc_geno 0.1 Genotype missingess
qc_hwe 1e-15 Hardy-Weinberg equilibrium (HWE) filter
qc_mind 0.1 Sample missigness
Option Default Description
vcf_conversion_split_id false If false, family and individual IDs are set to the sample ID (using plink2 --double-id option). If true, split VCF by “_” into FID and IID (--id-delim)

Prediction Step (Regenie Step 1)

The following parameters are all regenie specific. Please click here to learn more about them.

Option Default Description
regenie_skip_predictions false Skip regenie Step 1 predictions
regenie_force_step1 false Run regenie step 1 when >1M genotyped variants are used (not recommended)
regenie_bsize_step1 1000 Size of the genotype blocks
regenie_step1_optional null Add optional regenie step 1 params not directly supported

Single-variant and Gene-based Tests (Regenie Step 2)

The following parameters are all regenie specific. Please click here to learn more about them.

Option Default Description
regenie_bsize_step2 400 Size of the genotype blocks
regenie_firth true Use Firth likelihood ratio test (LRT) as fallback for p-values less than threshold
regenie_firth_approx true Use approximate Firth LRT for computational speedup
regenie_step2_optional null Add optional regenie step 2 params not directly supported

Single-variant Tests Only

Option Default Description
regenie_sample_file empty Sample file corresponding to input BGEN file
regenie_min_imputation_score 0.00 Minimum imputation info score (IMPUTE/MACH R^2)
regenie_min_mac 5 Minimum minor allele count
regenie_ref_first false Specify to use the first allele as the reference allele for BGEN or PLINK bed/bim/fam file input [default is to use the last allele as the reference]

Gene-based Tests Only

The following gene-based parameters are all regenie specific. Please click here to learn more about this feature.

Option Default Description
regenie_gene_aaf 1 % comma-separated list of AAF upper bounds to use when building masks
regenie_gene_test - comma-separated list of SKAT/ACAT-type tests to run
regenie_gene_joint - comma-separated list of joint tests to apply on the generated burden masks
regenie_gene_build_mask max build masks using the maximum number of ALT alleles across sites, or the sum of ALT alleles (‘sum’), or thresholding the sum to 2 (‘comphet’)
regenie_write_bed_masks - write mask to PLINK bed format (does not work when building masks with ‘sum’)
regenie_gene_vc_mac_thr 10 MAC threshold below which to collapse variants in SKAT/ACAT-type tests
regenie_gene_vc_max_aaf 100% AAF upper bound to use for SKAT/ACAT-type tests

Interaction Tests Only

The following interaction test parameters are all regenie specific. Please click here to learn more about this feature.

Option Default Description
regenie_rare_mac 1000 minor allele count (MAC) threshold below which to use HLM method for QTs
regenie_no_condtl false to print out all the main effects from the interaction model
regenie_force_condtl false to include the interacting SNP as a covariate in the marginal test