sentieon-cli-nf/nextflow.config at main · Elembio/sentieon-cli-nf · 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
130
params {
    // input + output
    input                      = null
    outdir                     = './results'

    // References
    genome                     = 'GRCh38'

    // samples
    ignore_samples             = ["Unassigned", "PhiX", "phiX", "CBPhiX", "Undetermined"]

    // Boilerplate options
    tracedir                   = "${params.outdir}/pipeline_info"
    enable_conda               = false
    igenomes_base              = "s3://ngi-igenomes/igenomes"
    igenomes_ignore            = false

    // sentieon
    sentieon_license           = System.getenv('SENTIEON_LICENSE') ?: null
    sentieon_ml_model          = "https://s3.amazonaws.com/sentieon-release/other/DNAscopeElementBioWGS2.0.bundle"
    assay                      = "WGS"
    target_region_bed          = null
    pcr                        = true

    // containers
    sentieoncli_container_url  = 'docker.io/sentieon/sentieon-cli'
    sentieoncli_container_tag  = 'v1.1.0-2'

    // nextflow
    publish_dir_mode           = 'copy'

    // sample batching
    batch_size                 = -1

    // Config options
    custom_config_version      = "main"
    custom_config_base         = "https://raw.githubusercontent.com/Elembio/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    max_multiqc_email_size     = '25.MB'
    multiqc_logo               = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '144.GB'
    max_cpus                   = 72
    max_time                   = '48.h'
}

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

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load custom config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load sentieon_cli_nf custom profiles from ElemBio
try {
    includeConfig "${params.custom_config_base}/pipeline/sentieon_cli_nf.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load pipeline config profile: ${params.custom_config_base}/pipeline/sentieon_cli_nf.config")
}

manifest {
    name            = 'elembio/sentieon-cli-nf'
    author          = 'Bryan R Lajoie, Carlos Ruiz Perez, Rosi Bajari, Max Mass'
    homePage        = 'https://gitlab.com/elembio/analysis/nextflow-workflows/sentieon-cli-nf'
    description     = 'sentieon-cli-nf'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=24.0.0'
    version         = '0.9.0'
}

profiles {
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }

    test { includeConfig 'conf/test.config' }
    test_small { includeConfig 'conf/test_small.config' }
    test_small_SE { includeConfig 'conf/test_small_SE.config' }
    test_trinity_idt { includeConfig 'conf/test_trinity_idt.config' }
    test_trinity_twist { includeConfig 'conf/test_trinity_twist.config' }
    local { includeConfig 'conf/local.config' }
    genome { includeConfig 'conf/genome.config' }
    exome { includeConfig 'conf/exome.config' }
}


// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry   = 'quay.io'
docker.registry      = 'quay.io'
podman.registry      = 'quay.io'
singularity.registry = 'quay.io'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}

// Define check_max function
def check_max(value, resource_type) {
    // Replace this logic with your actual maximum limit checks
    def max_limit = (resource_type == 'cpus') ? 64 : (resource_type == 'memory' ? 128.GB : null)
    return value > max_limit ? max_limit : value
}