Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/nextflow.config @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
parents
children 17890124001d
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@101 25 // Include modules' conig 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@101 58 docker.enabled = false
kkonganti@101 59 }
kkonganti@101 60
kkonganti@101 61 raven {
kkonganti@101 62 process.executor = 'slurm'
kkonganti@101 63 process.queue = 'prod'
kkonganti@101 64 process.memory = '10GB'
kkonganti@101 65 process.cpus = 4
kkonganti@101 66 params.enable_conda = false
kkonganti@101 67 params.enable_module = true
kkonganti@101 68 singularity.enabled = false
kkonganti@101 69 docker.enabled = false
kkonganti@101 70 clusterOptions = '--signal B:USR2'
kkonganti@101 71 }
kkonganti@101 72
kkonganti@101 73 eprod {
kkonganti@101 74 process.executor = 'slurm'
kkonganti@101 75 process.queue = 'lowmem,midmem,bigmem'
kkonganti@101 76 process.memory = '10GB'
kkonganti@101 77 process.cpus = 4
kkonganti@101 78 params.enable_conda = false
kkonganti@101 79 params.enable_module = true
kkonganti@101 80 singularity.enabled = false
kkonganti@101 81 docker.enabled = false
kkonganti@101 82 clusterOptions = '--signal B:USR2'
kkonganti@101 83 }
kkonganti@101 84
kkonganti@101 85 cingularity {
kkonganti@101 86 process.executor = 'slurm'
kkonganti@101 87 process.queue = 'prod'
kkonganti@101 88 process.memory = '10GB'
kkonganti@101 89 process.cpus = 4
kkonganti@101 90 singularity.enabled = true
kkonganti@101 91 singularity.autoMounts = true
kkonganti@101 92 docker.enabled = false
kkonganti@101 93 params.enable_conda = false
kkonganti@101 94 params.enable_module = false
kkonganti@101 95 clusterOptions = '--signal B:USR2'
kkonganti@101 96 }
kkonganti@101 97
kkonganti@101 98 cingularitygac {
kkonganti@101 99 process.executor = 'slurm'
kkonganti@101 100 executor.$slurm.exitReadTimeout = 120000
kkonganti@101 101 process.queue = 'centriflaken'
kkonganti@101 102 process.cpus = 4
kkonganti@101 103 singularity.enabled = true
kkonganti@101 104 singularity.autoMounts = true
kkonganti@101 105 docker.enabled = false
kkonganti@101 106 params.enable_conda = false
kkonganti@101 107 params.enable_module = false
kkonganti@101 108 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101 109 }
kkonganti@101 110
kkonganti@101 111 konda {
kkonganti@101 112 process.executor = 'slurm'
kkonganti@101 113 process.queue = 'prod'
kkonganti@101 114 process.memory = '10GB'
kkonganti@101 115 process.cpus = 4
kkonganti@101 116 singularity.enabled = false
kkonganti@101 117 docker.enabled = false
kkonganti@101 118 params.enable_conda = true
kkonganti@101 119 params.enable_module = false
kkonganti@101 120 clusterOptions = '--signal B:USR2'
kkonganti@101 121 }
kkonganti@101 122
kkonganti@101 123 kondagac {
kkonganti@101 124 process.executor = 'slurm'
kkonganti@101 125 executor.$slurm.exitReadTimeout = 120000
kkonganti@101 126 process.queue = 'centriflaken'
kkonganti@101 127 process.cpus = 4
kkonganti@101 128 singularity.enabled = false
kkonganti@101 129 docker.enabled = false
kkonganti@101 130 params.enable_conda = true
kkonganti@101 131 params.enable_module = false
kkonganti@101 132 clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101 133 }
kkonganti@101 134 }