kkonganti@0: def fs = File.separator
kkonganti@0: def pd = "${projectDir}"
kkonganti@0: 
kkonganti@0: // Global parameters
kkonganti@0: includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@0: includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@0: 
kkonganti@0: // Include FASTQ config to prepare for a case when the entry point is 
kkonganti@0: // FASTQ metadata CSV or FASTQ input directory
kkonganti@0: includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@0: 
kkonganti@0: if (params.pipeline != null) {
kkonganti@0:     try {
kkonganti@0:         includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@0:     } catch (Exception e) {
kkonganti@0:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@0:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@0:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@0:             "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@0:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@0:         System.exit(1)
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: // Include modules' conig last.
kkonganti@0: includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@0: includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@0: 
kkonganti@0: // Nextflow runtime profiles
kkonganti@38: conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
kkonganti@38: singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
kkonganti@0: 
kkonganti@0: profiles {
kkonganti@0:     standard {
kkonganti@0:         process.executor = 'local'
kkonganti@0:         process.cpus = 1
kkonganti@0:         params.enable_conda = false
kkonganti@0:         params.enable_module = true
kkonganti@0:         singularity.enabled = false
kkonganti@0:         docker.enabled = false
kkonganti@0:     }
kkonganti@0: 
kkonganti@7:     stdkondagac {
kkonganti@7:         process.executor = 'local'
kkonganti@7:         process.cpus = 4
kkonganti@7:         params.enable_conda = true
kkonganti@7:         params.enable_module = false
kkonganti@7:         singularity.enabled = false
kkonganti@7:         docker.enabled = false
kkonganti@7:     }
kkonganti@7: 
kkonganti@7:     stdcingularitygac {
kkonganti@7:         process.executor = 'local'
kkonganti@7:         process.cpus = 4
kkonganti@7:         params.enable_conda = false
kkonganti@7:         params.enable_module = false
kkonganti@7:         singularity.enabled = true
kkonganti@7:         docker.enabled = false
kkonganti@7:     }
kkonganti@7: 
kkonganti@0:     raven {
kkonganti@0:         process.executor = 'slurm'
kkonganti@0:         process.queue = 'prod'
kkonganti@0:         process.memory = '10GB'
kkonganti@0:         process.cpus = 4
kkonganti@0:         params.enable_conda = false
kkonganti@0:         params.enable_module = true
kkonganti@0:         singularity.enabled = false
kkonganti@0:         docker.enabled = false
kkonganti@0:         clusterOptions = '--signal B:USR2'
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     cingularity {
kkonganti@0:         process.executor = 'slurm'
kkonganti@0:         process.queue = 'prod'
kkonganti@0:         process.memory = '10GB'
kkonganti@0:         process.cpus = 4
kkonganti@0:         singularity.enabled = true
kkonganti@0:         singularity.autoMounts = true
kkonganti@0:         docker.enabled = false
kkonganti@0:         params.enable_conda = false
kkonganti@0:         params.enable_module = false
kkonganti@0:         clusterOptions = '--signal B:USR2'
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     cingularitygac {
kkonganti@0:         process.executor = 'slurm'
kkonganti@7:         executor.$slurm.exitReadTimeout = 60000
kkonganti@17:         process.queue = 'q8cpu'
kkonganti@0:         process.cpus = 4
kkonganti@0:         singularity.enabled = true
kkonganti@0:         singularity.autoMounts = true
kkonganti@0:         docker.enabled = false
kkonganti@0:         params.enable_conda = false
kkonganti@0:         params.enable_module = false
kkonganti@0:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     konda {
kkonganti@0:         process.executor = 'slurm'
kkonganti@0:         process.queue = 'prod'
kkonganti@0:         process.memory = '10GB'
kkonganti@0:         process.cpus = 4
kkonganti@0:         singularity.enabled = false
kkonganti@0:         docker.enabled = false
kkonganti@0:         params.enable_conda = true
kkonganti@0:         params.enable_module = false
kkonganti@0:         clusterOptions = '--signal B:USR2'
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     kondagac {
kkonganti@0:         process.executor = 'slurm'
kkonganti@7:         executor.$slurm.exitReadTimeout = 60000
kkonganti@17:         process.queue = 'q8cpu'
kkonganti@0:         process.cpus = 4
kkonganti@0:         singularity.enabled = false
kkonganti@0:         docker.enabled = false
kkonganti@0:         params.enable_conda = true
kkonganti@0:         params.enable_module = false
kkonganti@0:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@0:     }
kkonganti@0: }