Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/nextflow.config @ 118:a646fee152da

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 11:28:32 -0400
parents 77672281b19b
children d8662bd297b9
rev   line source
kkonganti@105 1 def fs = File.separator
kkonganti@105 2 def pd = "${projectDir}"
kkonganti@105 3
kkonganti@105 4 // Global parameters
kkonganti@105 5 includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@105 6 includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@105 7
kkonganti@105 8 // Include FASTQ config to prepare for a case when the entry point is
kkonganti@105 9 // FASTQ metadata CSV or FASTQ input directory
kkonganti@105 10 includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@105 11
kkonganti@105 12 if (params.pipeline != null) {
kkonganti@105 13 try {
kkonganti@105 14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@105 15 } catch (Exception e) {
kkonganti@105 16 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@105 17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@105 18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@105 19 "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@105 20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@105 21 System.exit(1)
kkonganti@105 22 }
kkonganti@105 23 }
kkonganti@105 24
kkonganti@105 25 // Include modules' config last.
kkonganti@105 26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@105 27 includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@105 28
kkonganti@105 29 // Nextflow runtime profiles
kkonganti@105 30 conda.cacheDir = '/tmp'
kkonganti@105 31 singularity.cacheDir = '/tmp'
kkonganti@105 32
kkonganti@105 33 // Cleanup after running
kkonganti@117 34 cleanup = true
kkonganti@105 35
kkonganti@105 36 profiles {
kkonganti@105 37 standard {
kkonganti@105 38 process.executor = 'local'
kkonganti@105 39 process.cpus = 1
kkonganti@105 40 params.enable_conda = false
kkonganti@105 41 params.enable_module = true
kkonganti@105 42 singularity.enabled = false
kkonganti@105 43 docker.enabled = false
kkonganti@105 44 }
kkonganti@105 45
kkonganti@105 46 stdkondagac {
kkonganti@105 47 process.executor = 'local'
kkonganti@105 48 process.cpus = 4
kkonganti@105 49 params.enable_conda = true
kkonganti@105 50 params.enable_module = false
kkonganti@105 51 singularity.enabled = false
kkonganti@105 52 docker.enabled = false
kkonganti@105 53 }
kkonganti@105 54
kkonganti@105 55 stdcingularitygac {
kkonganti@105 56 process.executor = 'local'
kkonganti@105 57 process.cpus = 4
kkonganti@105 58 params.enable_conda = false
kkonganti@105 59 params.enable_module = false
kkonganti@105 60 singularity.enabled = true
kkonganti@105 61 singularity.autoMounts = true
kkonganti@105 62 docker.enabled = false
kkonganti@105 63 }
kkonganti@105 64
kkonganti@105 65 raven {
kkonganti@105 66 process.executor = 'slurm'
kkonganti@105 67 process.queue = 'prod'
kkonganti@105 68 process.memory = '10GB'
kkonganti@105 69 process.cpus = 4
kkonganti@105 70 params.enable_conda = false
kkonganti@105 71 params.enable_module = true
kkonganti@105 72 singularity.enabled = false
kkonganti@105 73 docker.enabled = false
kkonganti@105 74 clusterOptions = '--signal B:USR2'
kkonganti@105 75 }
kkonganti@105 76
kkonganti@105 77 eprod {
kkonganti@105 78 process.executor = 'slurm'
kkonganti@105 79 process.queue = 'lowmem,midmem,bigmem'
kkonganti@105 80 process.memory = '10GB'
kkonganti@105 81 process.cpus = 4
kkonganti@105 82 params.enable_conda = false
kkonganti@105 83 params.enable_module = true
kkonganti@105 84 singularity.enabled = false
kkonganti@105 85 docker.enabled = false
kkonganti@105 86 clusterOptions = '--signal B:USR2'
kkonganti@105 87 }
kkonganti@105 88
kkonganti@105 89 eprodcingularity {
kkonganti@105 90 process.executor = 'slurm'
kkonganti@105 91 process.queue = 'lowmem,midmem,bigmem'
kkonganti@105 92 process.memory = '10GB'
kkonganti@105 93 process.cpus = 4
kkonganti@105 94 params.enable_conda = false
kkonganti@105 95 params.enable_module = false
kkonganti@105 96 singularity.enabled = true
kkonganti@105 97 singularity.autoMounts = true
kkonganti@105 98 docker.enabled = false
kkonganti@105 99 clusterOptions = '--signal B:USR2'
kkonganti@105 100 }
kkonganti@105 101
kkonganti@105 102 cingularity {
kkonganti@105 103 process.executor = 'slurm'
kkonganti@105 104 process.queue = 'prod'
kkonganti@105 105 process.memory = '10GB'
kkonganti@105 106 process.cpus = 4
kkonganti@105 107 singularity.enabled = true
kkonganti@105 108 singularity.autoMounts = true
kkonganti@105 109 docker.enabled = false
kkonganti@105 110 params.enable_conda = false
kkonganti@105 111 params.enable_module = false
kkonganti@105 112 clusterOptions = '--signal B:USR2'
kkonganti@105 113 }
kkonganti@105 114
kkonganti@105 115 cingularitygac {
kkonganti@105 116 process.executor = 'slurm'
kkonganti@105 117 executor.$slurm.exitReadTimeout = 120000
kkonganti@105 118 process.queue = 'centriflaken'
kkonganti@105 119 process.cpus = 4
kkonganti@105 120 singularity.enabled = true
kkonganti@105 121 singularity.autoMounts = true
kkonganti@105 122 docker.enabled = false
kkonganti@105 123 params.enable_conda = false
kkonganti@105 124 params.enable_module = false
kkonganti@105 125 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@105 126 }
kkonganti@105 127
kkonganti@105 128 konda {
kkonganti@105 129 process.executor = 'slurm'
kkonganti@105 130 process.queue = 'prod'
kkonganti@105 131 process.memory = '10GB'
kkonganti@105 132 process.cpus = 4
kkonganti@105 133 singularity.enabled = false
kkonganti@105 134 docker.enabled = false
kkonganti@105 135 params.enable_conda = true
kkonganti@105 136 params.enable_module = false
kkonganti@105 137 clusterOptions = '--signal B:USR2'
kkonganti@105 138 }
kkonganti@105 139
kkonganti@105 140 kondagac {
kkonganti@105 141 process.executor = 'slurm'
kkonganti@105 142 executor.$slurm.exitReadTimeout = 120000
kkonganti@105 143 process.queue = 'centriflaken'
kkonganti@105 144 process.cpus = 4
kkonganti@105 145 singularity.enabled = false
kkonganti@105 146 docker.enabled = false
kkonganti@105 147 params.enable_conda = true
kkonganti@105 148 params.enable_module = false
kkonganti@105 149 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@105 150 }
kkonganti@105 151
kkonganti@105 152 gxkubernetes {
kkonganti@105 153 process.executor = 'k8s'
kkonganti@105 154 k8s.namespace = 'galaxy'
kkonganti@113 155 k8s.serviceAccount = 'default'
kkonganti@116 156 k8s.maxErrorRetry = 3
kkonganti@117 157 k8s.storageMountPath = '/galaxy'
kkonganti@118 158 k8s.storageSubPath = '/galaxy'
kkonganti@105 159 singularity.enabled = false
kkonganti@105 160 docker.enabled = true
kkonganti@105 161 params.enable_conda = false
kkonganti@105 162 params.enable_module = false
kkonganti@105 163 }
kkonganti@105 164 }