cells2stats-nf/nextflow.config at main · Elembio/cells2stats-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
131
132
133
134
135
params {
    // Container

    container_url = "docker.io/elembio/cells2stats"
    container_tag = "latest"

    // Run
    run_dir = null
    id = null

    // Cells2Stats
    batch = ""
    error_on_missing = false
    log_level = "info"
    max_unassigned = null
    no_error_on_invalid = false
    panel = null
    run_manifest = null
    skip_cellprofiler = false
    tile = ""
    well = ""
    visualization = false
    visualization_only = false
    segmentation = null
    skip_html_report = false

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    enable_conda               = false
    publish_dir_mode           = 'copy'

    // 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

    // Max resources
    max_cpus                   = 48
    max_memory                 = '192.GB'
    max_time                   = '8.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 elembio/cell2stats custom profiles from different institutions.
try {
    includeConfig "${params.custom_config_base}/pipeline/cells2stats_nf.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load pipeline config profile: ${params.custom_config_base}/pipeline/cells2stats_nf.config")
}

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

manifest {
    name            = 'elembio/cells2stats'
    author          = 'Carlos A Ruiz, Bryan R Lajoie'
    homePage        = 'https://gitlab.com/elembio/analysis/nextflow-workflows/cells2stats-nf'
    description     = 'Cell stats generation from Element AVITI24 System'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '1.0.0'
}

// 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'

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

    test { includeConfig 'conf/test.config' }
    local { includeConfig 'conf/local.config' }
    tower { includeConfig 'conf/tower.config' }
    tower_spot { includeConfig 'conf/tower_spot.config' }
    ElembioCloud { includeConfig 'conf/ElembioCloud.config'}
    notaskdir { includeConfig 'conf/notaskdir.config'}
}

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

def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}