configs/conf/uppmax.config at 2b8a755edf1bcc47a0360b14d8eaec2b173fd5c6 · nf-core/configs · 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
// UPPMAX Config Profile
// Docs: https://github.com/nf-core/configs/blob/master/docs/uppmax.md
// Supported clusters:
// - Bianca
// - Miarka
// - Rackham
// - Snowy
// - Pelle

params {
    // Description is overwritten for other clusters using includeConfig
    config_profile_description   = 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
    config_profile_contact       = 'Phil Ewels (@ewels)'
    config_profile_url           = 'https://www.uppmax.uu.se/'
    project                      = null
    clusterOptions               = null
    schema_ignore_params         = "genomes,input_paths,cluster-options,clusterOptions,project"
    validationSchemaIgnoreParams = "genomes,input_paths,cluster-options,clusterOptions,project,schema_ignore_params"
    save_reference               = true
    // Defaults set for Bianca - other clusters set using includeConfig below
    max_memory                   = 500.GB
    max_cpus                     = 16
    max_time                     = 240.h
    // illumina iGenomes reference file paths on UPPMAX
    igenomes_base                = '/sw/data/igenomes/'
    ignore_params_list           = [
        "cluster-options",
        "clusterOptions",
        "clusterName",
        "genomes",
        "ignore_params_list",
        "input_paths",
        "max_cpus",
        "max_memory",
        "max_time",
        "project",
        "schema_ignore_params",
        "validationSchemaIgnoreParams",
    ]
}

// nf-schema/nf-validation settings
// Different versions use different specifications
validation {
    ignoreParams = params.ignore_params_list
}
params.schema_ignore_params = params.ignore_params_list.join(",")
params.validationSchemaIgnoreParams = params.ignore_params_list.join(",")

singularity {
    enabled      = true
    envWhitelist = 'SNIC_TMP'
}

executor {
    $slurm {
        account = params.project
    }
}

// Hardware: https://docs.uppmax.uu.se/hardware/clusters/bianca/
process {
    resourceLimits = [
        memory: 500.GB,
        cpus: 16,
        time: 240.h,
    ]
    clusterOptions = {
        [
            "-A ${params.project}",
            params.clusterOptions ?: "",
            task.memory > 250.GB
                ? "-p node -C mem512GB"
                : "",
        ].minus("").join(" ")
    }
    executor       = 'slurm'
    // Use node local storage for execution.
    scratch        = '$SNIC_TMP'
}

// Overwrite settings depending on cluster
includeConfig ({
    def cluster = "unknown"
    try {
        cluster = ['/bin/bash', '-c', "sacctmgr show cluster -P -n | cut -f1 -d'|' | grep 'miarka\\|pelle\\|rackham'"].execute().text.trim()
    }
    catch (IOException _e) {
        System.err.println("WARNING: Could not run sacctmgr, defaulting to unknown")
    }
    if (cluster == "rackham") {
        if (params.clusterOptions != null && params.clusterOptions.contains('-M snowy')) {
            return "uppmax/snowy.config"
        }
        else {
            return "uppmax/rackham.config"
        }
    }
    else if (cluster == "pelle") {
        return "uppmax/pelle.config"
    }
    else if (cluster == "miarka") {
        return "uppmax/miarka.config"
    }
    return "/dev/null"
}.call())

// Additional devel profile for running in devel queue
// Run with `-profile uppmax,devel`
profiles {
    devel {
        params {
            config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
            // Max resources to be requested by a devel job
            max_memory                 = 120.GB
            max_time                   = 1.h
        }
        executor.queueSize = 1
        process {
            queue          = 'devel'
            resourceLimits = [
                memory: 120.GB,
                cpus: 4,
                time: 1.h,
            ]
        }
    }
}