Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/nextflow.config @ 104:17890124001d

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"planemo upload"
author kkonganti
date Sun, 28 Aug 2022 00:37:10 -0400
parents ce6d9548fe89
children
rev   line source
kkonganti@101 1 def fs = File.separator
kkonganti@101 2 def pd = "${projectDir}"
kkonganti@101 3
kkonganti@101 4 // Global parameters
kkonganti@101 5 includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@101 6 includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@101 7
kkonganti@101 8 // Include FASTQ config to prepare for a case when the entry point is
kkonganti@101 9 // FASTQ metadata CSV or FASTQ input directory
kkonganti@101 10 includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@101 11
kkonganti@101 12 if (params.pipeline != null) {
kkonganti@101 13 try {
kkonganti@101 14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@101 15 } catch (Exception e) {
kkonganti@101 16 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@101 17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@101 18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@101 19 "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@101 20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@101 21 System.exit(1)
kkonganti@101 22 }
kkonganti@101 23 }
kkonganti@101 24
kkonganti@104 25 // Include modules' config last.
kkonganti@101 26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@101 27 includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@101 28
kkonganti@101 29 // Nextflow runtime profiles
kkonganti@101 30 conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
kkonganti@101 31 singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
kkonganti@101 32
kkonganti@101 33 profiles {
kkonganti@101 34 standard {
kkonganti@101 35 process.executor = 'local'
kkonganti@101 36 process.cpus = 1
kkonganti@101 37 params.enable_conda = false
kkonganti@101 38 params.enable_module = true
kkonganti@101 39 singularity.enabled = false
kkonganti@101 40 docker.enabled = false
kkonganti@101 41 }
kkonganti@101 42
kkonganti@101 43 stdkondagac {
kkonganti@101 44 process.executor = 'local'
kkonganti@101 45 process.cpus = 4
kkonganti@101 46 params.enable_conda = true
kkonganti@101 47 params.enable_module = false
kkonganti@101 48 singularity.enabled = false
kkonganti@101 49 docker.enabled = false
kkonganti@101 50 }
kkonganti@101 51
kkonganti@101 52 stdcingularitygac {
kkonganti@101 53 process.executor = 'local'
kkonganti@101 54 process.cpus = 4
kkonganti@101 55 params.enable_conda = false
kkonganti@101 56 params.enable_module = false
kkonganti@101 57 singularity.enabled = true
kkonganti@104 58 singularity.autoMounts = true
kkonganti@101 59 docker.enabled = false
kkonganti@101 60 }
kkonganti@101 61
kkonganti@101 62 raven {
kkonganti@101 63 process.executor = 'slurm'
kkonganti@101 64 process.queue = 'prod'
kkonganti@101 65 process.memory = '10GB'
kkonganti@101 66 process.cpus = 4
kkonganti@101 67 params.enable_conda = false
kkonganti@101 68 params.enable_module = true
kkonganti@101 69 singularity.enabled = false
kkonganti@101 70 docker.enabled = false
kkonganti@101 71 clusterOptions = '--signal B:USR2'
kkonganti@101 72 }
kkonganti@101 73
kkonganti@101 74 eprod {
kkonganti@101 75 process.executor = 'slurm'
kkonganti@101 76 process.queue = 'lowmem,midmem,bigmem'
kkonganti@101 77 process.memory = '10GB'
kkonganti@101 78 process.cpus = 4
kkonganti@101 79 params.enable_conda = false
kkonganti@101 80 params.enable_module = true
kkonganti@101 81 singularity.enabled = false
kkonganti@101 82 docker.enabled = false
kkonganti@101 83 clusterOptions = '--signal B:USR2'
kkonganti@101 84 }
kkonganti@101 85
kkonganti@104 86 eprodcingularity {
kkonganti@104 87 process.executor = 'slurm'
kkonganti@104 88 process.queue = 'lowmem,midmem,bigmem'
kkonganti@104 89 process.memory = '10GB'
kkonganti@104 90 process.cpus = 4
kkonganti@104 91 params.enable_conda = false
kkonganti@104 92 params.enable_module = false
kkonganti@104 93 singularity.enabled = true
kkonganti@104 94 singularity.autoMounts = true
kkonganti@104 95 docker.enabled = false
kkonganti@104 96 clusterOptions = '--signal B:USR2'
kkonganti@104 97 }
kkonganti@104 98
kkonganti@101 99 cingularity {
kkonganti@101 100 process.executor = 'slurm'
kkonganti@101 101 process.queue = 'prod'
kkonganti@101 102 process.memory = '10GB'
kkonganti@101 103 process.cpus = 4
kkonganti@101 104 singularity.enabled = true
kkonganti@101 105 singularity.autoMounts = true
kkonganti@101 106 docker.enabled = false
kkonganti@101 107 params.enable_conda = false
kkonganti@101 108 params.enable_module = false
kkonganti@101 109 clusterOptions = '--signal B:USR2'
kkonganti@101 110 }
kkonganti@101 111
kkonganti@101 112 cingularitygac {
kkonganti@101 113 process.executor = 'slurm'
kkonganti@101 114 executor.$slurm.exitReadTimeout = 120000
kkonganti@101 115 process.queue = 'centriflaken'
kkonganti@101 116 process.cpus = 4
kkonganti@101 117 singularity.enabled = true
kkonganti@101 118 singularity.autoMounts = true
kkonganti@101 119 docker.enabled = false
kkonganti@101 120 params.enable_conda = false
kkonganti@101 121 params.enable_module = false
kkonganti@101 122 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101 123 }
kkonganti@101 124
kkonganti@101 125 konda {
kkonganti@101 126 process.executor = 'slurm'
kkonganti@101 127 process.queue = 'prod'
kkonganti@101 128 process.memory = '10GB'
kkonganti@101 129 process.cpus = 4
kkonganti@101 130 singularity.enabled = false
kkonganti@101 131 docker.enabled = false
kkonganti@101 132 params.enable_conda = true
kkonganti@101 133 params.enable_module = false
kkonganti@101 134 clusterOptions = '--signal B:USR2'
kkonganti@101 135 }
kkonganti@101 136
kkonganti@101 137 kondagac {
kkonganti@101 138 process.executor = 'slurm'
kkonganti@101 139 executor.$slurm.exitReadTimeout = 120000
kkonganti@101 140 process.queue = 'centriflaken'
kkonganti@101 141 process.cpus = 4
kkonganti@101 142 singularity.enabled = false
kkonganti@101 143 docker.enabled = false
kkonganti@101 144 params.enable_conda = true
kkonganti@101 145 params.enable_module = false
kkonganti@101 146 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101 147 }
kkonganti@101 148 }