imputationserver2/nextflow.config at statgen-custom-changes · statgen/imputationserver2 · GitHub

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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
manifest {
    name            = 'imputationserver2'
    version         = '2.0.13-statgen.1'
    description     = 'Genotype Imputation Server 2'
    author          = 'Imputation Server Team'
    homePage        = 'https://github.com/statgen/imputationserver2'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
}

// Global default params, used in configs
params {

    project                     = null
    project_date                = "`date`"
    files                       = null
    allele_frequency_population = null
    refpanel_yaml               = null

    mode          = 'imputation'
    chunksize     = 20_000_000
    min_samples   = 20
    max_samples   = 50_000
    merge_results = true
    password      = null
    send_mail     = false

    service = [
        name    : 'TOPMed Imputation Server',
        contact : null,
        email   : null,
        url     : null,
        threads : -1,
    ]

    user = [
        name  : null,
        email : null,
    ]

    phasing = [
        engine : 'eagle',
        window : 5_000_000,
    ]

    imputation = [
        enabled           : true,
        window            : 500_000,
        minimac_min_ratio : 0.00001,
        min_r2            : 0,
        meta              : false,
        md5               : false,
        create_index      : false,
        decay             : 0,
        prob_threshold    : -1,
        prob_threshold_s1 : -1,
        diff_threshold    : -1,
        min_recom         : -1,
    ]

    encryption = [
        enabled      : true,
        aes          : false,
        annotate     : true,
        thread_scale : 1,
    ]

    ancestry = [
        enabled    : false,
        dim        : 10,
        dim_high   : 20,
        batch_size : 50,
        reference  : null,
        max_pcs    : 8,
        k          : 10,
        threshold  : 0.75,
    ]

    pgs = [
        enabled          : false,
        min_r2           : 0,
        fix_strand_flips : false,
        category         : "all",
    ]

    pgscatalog = [
        scores : "",
        meta   : "",
    ]

}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }

    docker.enabled             = true
    singularity.enabled        = false
    process.container          = 'public.ecr.aws/z4i9d6e2/statgen:v2.0.13-statgen.1'

    development {
        process.container      = 'statgen/imputationserver2:latest'
        docker.enabled         = true
        resume                 = true
        singularity.enabled    = false
    }

    docker {
        docker.enabled         = true
        singularity.enabled    = false
    }

    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
    }

    slurm {
        process.executor       = 'slurm'
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
    }

   test { includeConfig 'conf/test.config' }
}