-
Notifications
You must be signed in to change notification settings - Fork 0
/
Config.config
52 lines (42 loc) · 1.38 KB
/
Config.config
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
includeConfig 'configs/local.config'
params.outdir = "$PWD/Results"
params.datdir = "$PWD/data"
params.pipeline_engine = "genesis"
// Genotype data input:
params.genodat_format = "gds"
params.vcf_list = "NA"
params.gds_list = "${params.datdir}/gds_list.csv"
params.genotype_or_dosage = "DS"
// PreQC parameters if run PreQC.nf
params.hwe_p = 0.05
params.min_mac = 3
params.max_missing_allowed = 0.1
// Phenotype input:
params.phenotype_file = "${params.datdir}/pheno_file.csv"
params.phenotype_names = "${params.datdir}/pheno_name.txt"
// Covariates:
params.covariates_file = "${params.phenotype_file}"
params.covariates = "age,sex,PC1,PC2,PC3,PC4"
params.covariates_factor = "sex"
// PCs and GRM input:
params.PC_rds = "NA"
params.GRM_rds = "${params.datdir}/grm.rds"
// Specific SNPs and Samples to analyze:
params.snpset_assoc_txtfile = "${params.datdir}/snpid_subset.txt"
params.userdef_sampleid_txtfile = "NA"
// optional workflow for PCA and GRM:
params.start_PC = false
params.snpset_PCA_txtfile = "NA"
params.pcair_kinthresh = 11
params.pcair_divthresh = 11
// Pipeline setups:
params.max_forks_parallel = 100
params.max_pheno_parallel = 100
params.pval_cutoff = 1
params.output_result_csv = "false"
// Plotting parameters:
params.draw_genopheno_boxplot = "true"
params.boxplot_p_cutoff = 5e-8
params.plot_mac = 3
params.plot_resolution = 100
params.plot_size = 400