kkonganti@92: def fs = File.separator
kkonganti@92: def pd = "${projectDir}"
kkonganti@92: 
kkonganti@92: // Global parameters
kkonganti@92: includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@92: includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@92: 
kkonganti@92: // Include FASTQ config to prepare for a case when the entry point is 
kkonganti@92: // FASTQ metadata CSV or FASTQ input directory
kkonganti@92: includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@92: 
kkonganti@92: if (params.pipeline != null) {
kkonganti@92:     try {
kkonganti@92:         includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@92:     } catch (Exception e) {
kkonganti@92:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@92:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@92:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@92:             "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@92:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@92:         System.exit(1)
kkonganti@92:     }
kkonganti@92: }
kkonganti@92: 
kkonganti@92: // Include modules' conig last.
kkonganti@92: includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@92: includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@92: 
kkonganti@92: // Nextflow runtime profiles
kkonganti@93: conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
kkonganti@93: singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
kkonganti@92: 
kkonganti@92: profiles {
kkonganti@92:     standard {
kkonganti@92:         process.executor = 'local'
kkonganti@92:         process.cpus = 1
kkonganti@92:         params.enable_conda = false
kkonganti@92:         params.enable_module = true
kkonganti@92:         singularity.enabled = false
kkonganti@92:         docker.enabled = false
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     stdkondagac {
kkonganti@92:         process.executor = 'local'
kkonganti@92:         process.cpus = 4
kkonganti@92:         params.enable_conda = true
kkonganti@92:         params.enable_module = false
kkonganti@92:         singularity.enabled = false
kkonganti@92:         docker.enabled = false
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     stdcingularitygac {
kkonganti@92:         process.executor = 'local'
kkonganti@92:         process.cpus = 4
kkonganti@92:         params.enable_conda = false
kkonganti@92:         params.enable_module = false
kkonganti@92:         singularity.enabled = true
kkonganti@92:         docker.enabled = false
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     raven {
kkonganti@92:         process.executor = 'slurm'
kkonganti@92:         process.queue = 'prod'
kkonganti@92:         process.memory = '10GB'
kkonganti@92:         process.cpus = 4
kkonganti@92:         params.enable_conda = false
kkonganti@92:         params.enable_module = true
kkonganti@92:         singularity.enabled = false
kkonganti@92:         docker.enabled = false
kkonganti@92:         clusterOptions = '--signal B:USR2'
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     cingularity {
kkonganti@92:         process.executor = 'slurm'
kkonganti@92:         process.queue = 'prod'
kkonganti@92:         process.memory = '10GB'
kkonganti@92:         process.cpus = 4
kkonganti@92:         singularity.enabled = true
kkonganti@92:         singularity.autoMounts = true
kkonganti@92:         docker.enabled = false
kkonganti@92:         params.enable_conda = false
kkonganti@92:         params.enable_module = false
kkonganti@92:         clusterOptions = '--signal B:USR2'
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     cingularitygac {
kkonganti@92:         process.executor = 'slurm'
kkonganti@92:         executor.$slurm.exitReadTimeout = 120000
kkonganti@92:         process.queue = 'q8cpu'
kkonganti@92:         process.cpus = 4
kkonganti@92:         singularity.enabled = true
kkonganti@92:         singularity.autoMounts = true
kkonganti@92:         docker.enabled = false
kkonganti@92:         params.enable_conda = false
kkonganti@92:         params.enable_module = false
kkonganti@92:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     konda {
kkonganti@92:         process.executor = 'slurm'
kkonganti@92:         process.queue = 'prod'
kkonganti@92:         process.memory = '10GB'
kkonganti@92:         process.cpus = 4
kkonganti@92:         singularity.enabled = false
kkonganti@92:         docker.enabled = false
kkonganti@92:         params.enable_conda = true
kkonganti@92:         params.enable_module = false
kkonganti@92:         clusterOptions = '--signal B:USR2'
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     kondagac {
kkonganti@92:         process.executor = 'slurm'
kkonganti@92:         executor.$slurm.exitReadTimeout = 120000
kkonganti@92:         process.queue = 'q8cpu'
kkonganti@92:         process.cpus = 4
kkonganti@92:         singularity.enabled = false
kkonganti@92:         docker.enabled = false
kkonganti@92:         params.enable_conda = true
kkonganti@92:         params.enable_module = false
kkonganti@92:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@92:     }
kkonganti@92: }