params.yml

---
# Input files
input: /home/amcalejandro/Data/WorkingDirectory/Development_Stuff/LONGWAS-NEXTFLOW/WORKSHOP/workdir/longitudinal-GWAS-pipeline/example/genotype/chr[1-3].vcf
covarfile: /home/amcalejandro/Data/WorkingDirectory/Development_Stuff/LONGWAS-NEXTFLOW/WORKSHOP/workdir/longitudinal-GWAS-pipeline/example/covariates.tsv
phenofile: /home/amcalejandro/Data/WorkingDirectory/Development_Stuff/LONGWAS-NEXTFLOW/WORKSHOP/workdir/longitudinal-GWAS-pipeline/example/phenotype.surv.tsv

#Variables names
pheno_name: surv_y
covariates: "SEX age_at_baseline"
#study_col: surv_y
time_col: study_days

# Model variables
longitudinal_flag: false
survival_flag: true
linear_flag: false
chunk_flag: true

# Parameters for genetic QC
r2thres: -9
minor_allele_freq: "0.05"
minor_allele_ct: "20"
kinship: "0.177"
ancestry: "EUR"
assembly: "hg19"
#Identifier for the input genotype files - useful to cache results
dataset: "V2_SURV"

# Generate manhattan with result files
mh_plot: true