Caeno_Scan/nextflow.config at main · AndersenLab/Caeno_Scan · 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
process.cache = 'deep'

nextflowVersion = '>=20.0'

import java.time.*
Date now = new Date()


params {
    day                = now.format("yyyMMdd")
    timestamp          = now.format("yyyyMMdd-HH-mm-ss")
    out                = "Analysis_Results-${day}"
}

profiles {

  //  mappings { includeConfig 'conf/mappings.config' }
  //  standard { includeConfig 'conf/mappings.config' }
  //  simulations { includeConfig 'conf/simulations.config' }
  //  gcp { includeConfig 'conf/gcp.config' }
  //  genomatrix { includeConfig 'conf/genomatrix.config' }
  //  local { includeConfig 'conf/local.config' }

}

report {
    enabled = true
    file = "${params.out}/${params.timestamp}_report.html"
}

timeline {
    enabled = true
    file = "${params.out}/${params.timestamp}_timeline.html"
}

//executor {
   // queueSize = 500
   // submitRateLimit = 5
  //  'local'
//}

//process.executor = 'local'
//process.container = 'andersenlab/nemascan:20220407173056db3227'
//docker.enabled = true

//process {
   // container = 'andersenlab/nemascan:20220407173056db3227'

  //  withLabel: mediation {
  //      container = 'andersenlab/mediation:20220407173046db3227'
  //  }
// }

process {
    executor = 'slurm'
    queue = 'genomicsguestA'
    clusterOptions = '-A b1042 -t 2:00:00 -e errlog.txt'
    queueSize = 100
    withLabel: sim_map_phenos {
        errorStrategy='retry'
        maxRetries=3
        container = 'andersenlab/mediation:20220407173046db3227'
  }
}
singularity {
    pullTimeout = '30 min'
    enabled = true
    autoMounts = true
    cacheDir = "/projects/b1059/singularity"
}

params {

      maps              = null
      simulate          = "RUN"
      matrix            = null
      annotate   = null
      simulate_maf      = "input_data/all_species/simulate_maf.csv"
      simulate_nqtl     = "input_data/all_species/simulate_nqtl.csv"
      simulate_reps     = 2
      simulate_h2       = "input_data/all_species/simulate_h2.csv"
      simulate_eff      = "input_data/all_species/simulate_effect_sizes.csv"
      simulate_strains  = "input_data/all_species/simulate_strains.tsv"
      simulate_qtlloc   = null
      eigen_mem = "110 GB"
      mediation = false
      sthresh = "BF"
}