Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/nextflow.config @ 140:7ab975454646

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planemo upload
author kkonganti
date Thu, 11 Jul 2024 12:47:02 -0400
parents c5daa29f933c
children 3bae471a5e14
rev   line source
kkonganti@130 1 def fs = File.separator
kkonganti@130 2 def pd = "${projectDir}"
kkonganti@130 3
kkonganti@130 4 // Global parameters
kkonganti@130 5 includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@130 6 includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@130 7
kkonganti@130 8 // Include FASTQ config to prepare for a case when the entry point is
kkonganti@130 9 // FASTQ metadata CSV or FASTQ input directory
kkonganti@130 10 includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@130 11
kkonganti@130 12 if (params.pipeline != null) {
kkonganti@130 13 try {
kkonganti@130 14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@130 15 } catch (Exception e) {
kkonganti@130 16 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@130 17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@130 18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@130 19 "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@130 20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@130 21 System.exit(1)
kkonganti@130 22 }
kkonganti@130 23 }
kkonganti@130 24
kkonganti@130 25 // Include modules' config last.
kkonganti@130 26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@130 27 includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@130 28
kkonganti@130 29 // Nextflow runtime profiles
kkonganti@130 30 conda.cacheDir = '/tmp'
kkonganti@130 31 singularity.cacheDir = '/tmp'
kkonganti@130 32
kkonganti@130 33 // Cleanup after running
kkonganti@130 34 cleanup = true
kkonganti@130 35
kkonganti@130 36 profiles {
kkonganti@130 37 standard {
kkonganti@130 38 process.executor = 'local'
kkonganti@130 39 process.cpus = 1
kkonganti@130 40 params.enable_conda = false
kkonganti@130 41 params.enable_module = true
kkonganti@130 42 singularity.enabled = false
kkonganti@130 43 docker.enabled = false
kkonganti@130 44 }
kkonganti@130 45
kkonganti@130 46 stdkondagac {
kkonganti@130 47 process.executor = 'local'
kkonganti@130 48 process.cpus = 4
kkonganti@130 49 params.enable_conda = true
kkonganti@130 50 params.enable_module = false
kkonganti@130 51 singularity.enabled = false
kkonganti@130 52 docker.enabled = false
kkonganti@130 53 }
kkonganti@130 54
kkonganti@130 55 stdcingularitygac {
kkonganti@130 56 process.executor = 'local'
kkonganti@130 57 process.cpus = 4
kkonganti@130 58 params.enable_conda = false
kkonganti@130 59 params.enable_module = false
kkonganti@130 60 singularity.enabled = true
kkonganti@130 61 singularity.autoMounts = true
kkonganti@130 62 docker.enabled = false
kkonganti@130 63 }
kkonganti@130 64
kkonganti@130 65 raven {
kkonganti@130 66 process.executor = 'slurm'
kkonganti@130 67 process.queue = 'prod'
kkonganti@130 68 process.memory = '10GB'
kkonganti@130 69 process.cpus = 4
kkonganti@130 70 params.enable_conda = false
kkonganti@130 71 params.enable_module = true
kkonganti@130 72 singularity.enabled = false
kkonganti@130 73 docker.enabled = false
kkonganti@130 74 clusterOptions = '--signal B:USR2'
kkonganti@130 75 }
kkonganti@130 76
kkonganti@130 77 eprod {
kkonganti@130 78 process.executor = 'slurm'
kkonganti@130 79 process.queue = 'lowmem,midmem,bigmem'
kkonganti@130 80 process.memory = '10GB'
kkonganti@130 81 process.cpus = 4
kkonganti@130 82 params.enable_conda = false
kkonganti@130 83 params.enable_module = true
kkonganti@130 84 singularity.enabled = false
kkonganti@130 85 docker.enabled = false
kkonganti@130 86 clusterOptions = '--signal B:USR2'
kkonganti@130 87 }
kkonganti@130 88
kkonganti@130 89 eprodcingularity {
kkonganti@130 90 process.executor = 'slurm'
kkonganti@130 91 process.queue = 'lowmem,midmem,bigmem'
kkonganti@130 92 process.memory = '10GB'
kkonganti@130 93 process.cpus = 4
kkonganti@130 94 params.enable_conda = false
kkonganti@130 95 params.enable_module = false
kkonganti@130 96 singularity.enabled = true
kkonganti@130 97 singularity.autoMounts = true
kkonganti@130 98 docker.enabled = false
kkonganti@130 99 clusterOptions = '--signal B:USR2'
kkonganti@130 100 }
kkonganti@130 101
kkonganti@130 102 cingularity {
kkonganti@130 103 process.executor = 'slurm'
kkonganti@130 104 process.queue = 'prod'
kkonganti@130 105 process.memory = '10GB'
kkonganti@130 106 process.cpus = 4
kkonganti@130 107 singularity.enabled = true
kkonganti@130 108 singularity.autoMounts = true
kkonganti@130 109 docker.enabled = false
kkonganti@130 110 params.enable_conda = false
kkonganti@130 111 params.enable_module = false
kkonganti@130 112 clusterOptions = '--signal B:USR2'
kkonganti@130 113 }
kkonganti@130 114
kkonganti@130 115 cingularitygac {
kkonganti@130 116 process.executor = 'slurm'
kkonganti@130 117 executor.$slurm.exitReadTimeout = 120000
kkonganti@130 118 process.queue = 'centriflaken'
kkonganti@130 119 process.cpus = 4
kkonganti@130 120 singularity.enabled = true
kkonganti@130 121 singularity.autoMounts = true
kkonganti@130 122 docker.enabled = false
kkonganti@130 123 params.enable_conda = false
kkonganti@130 124 params.enable_module = false
kkonganti@130 125 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@130 126 }
kkonganti@130 127
kkonganti@130 128 konda {
kkonganti@130 129 process.executor = 'slurm'
kkonganti@130 130 process.queue = 'prod'
kkonganti@130 131 process.memory = '10GB'
kkonganti@130 132 process.cpus = 4
kkonganti@130 133 singularity.enabled = false
kkonganti@130 134 docker.enabled = false
kkonganti@130 135 params.enable_conda = true
kkonganti@130 136 params.enable_module = false
kkonganti@130 137 clusterOptions = '--signal B:USR2'
kkonganti@130 138 }
kkonganti@130 139
kkonganti@130 140 kondagac {
kkonganti@130 141 process.executor = 'slurm'
kkonganti@130 142 executor.$slurm.exitReadTimeout = 120000
kkonganti@130 143 process.queue = 'centriflaken'
kkonganti@130 144 process.cpus = 4
kkonganti@130 145 singularity.enabled = false
kkonganti@130 146 docker.enabled = false
kkonganti@130 147 params.enable_conda = true
kkonganti@130 148 params.enable_module = false
kkonganti@130 149 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@130 150 }
kkonganti@130 151
kkonganti@130 152 gxkubernetes {
kkonganti@130 153 process.executor = 'k8s'
kkonganti@130 154 k8s.namespace = 'galaxy'
kkonganti@130 155 k8s.serviceAccount = 'default'
kkonganti@140 156 k8s.computeResourceType = 'Job'
kkonganti@130 157 k8s.pod = [
kkonganti@130 158 [volumeClaim: 's3-centriflaken-claim', mountPath: '/galaxy/cfsan-centriflaken-db'],
kkonganti@130 159 [volumeClaim: 's3-nextflow-claim', mountPath: '/galaxy/nf-work-dirs'],
kkonganti@139 160 [volumeClaim: 'galaxy-galaxy-pvc', mountPath: '/galaxy/server/database'],
kkonganti@139 161 [priorityClassName: 'galaxy-job-priority']
kkonganti@130 162 ]
kkonganti@130 163 singularity.enabled = false
kkonganti@130 164 docker.enabled = true
kkonganti@130 165 params.enable_conda = false
kkonganti@130 166 params.enable_module = false
kkonganti@130 167 }
kkonganti@130 168 }