kkonganti@101: def fs = File.separator
kkonganti@101: def pd = "${projectDir}"
kkonganti@101: 
kkonganti@101: // Global parameters
kkonganti@101: includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@101: includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@101: 
kkonganti@101: // Include FASTQ config to prepare for a case when the entry point is 
kkonganti@101: // FASTQ metadata CSV or FASTQ input directory
kkonganti@101: includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@101: 
kkonganti@101: if (params.pipeline != null) {
kkonganti@101:     try {
kkonganti@101:         includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@101:     } catch (Exception e) {
kkonganti@101:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@101:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@101:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@101:             "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@101:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@101:         System.exit(1)
kkonganti@101:     }
kkonganti@101: }
kkonganti@101: 
kkonganti@104: // Include modules' config last.
kkonganti@101: includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@101: includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@101: 
kkonganti@101: // Nextflow runtime profiles
kkonganti@101: conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
kkonganti@101: singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
kkonganti@101: 
kkonganti@101: profiles {
kkonganti@101:     standard {
kkonganti@101:         process.executor = 'local'
kkonganti@101:         process.cpus = 1
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = true
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     stdkondagac {
kkonganti@101:         process.executor = 'local'
kkonganti@101:         process.cpus = 4
kkonganti@101:         params.enable_conda = true
kkonganti@101:         params.enable_module = false
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     stdcingularitygac {
kkonganti@101:         process.executor = 'local'
kkonganti@101:         process.cpus = 4
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = false
kkonganti@101:         singularity.enabled = true
kkonganti@104:         singularity.autoMounts = true
kkonganti@101:         docker.enabled = false
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     raven {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         process.queue = 'prod'
kkonganti@101:         process.memory = '10GB'
kkonganti@101:         process.cpus = 4
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = true
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:         clusterOptions = '--signal B:USR2'
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     eprod {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         process.queue = 'lowmem,midmem,bigmem'
kkonganti@101:         process.memory = '10GB'
kkonganti@101:         process.cpus = 4
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = true
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:         clusterOptions = '--signal B:USR2'
kkonganti@101:     }
kkonganti@101: 
kkonganti@104:     eprodcingularity {
kkonganti@104:         process.executor = 'slurm'
kkonganti@104:         process.queue = 'lowmem,midmem,bigmem'
kkonganti@104:         process.memory = '10GB'
kkonganti@104:         process.cpus = 4
kkonganti@104:         params.enable_conda = false
kkonganti@104:         params.enable_module = false
kkonganti@104:         singularity.enabled = true
kkonganti@104:         singularity.autoMounts = true
kkonganti@104:         docker.enabled = false
kkonganti@104:         clusterOptions = '--signal B:USR2'
kkonganti@104:     }
kkonganti@104: 
kkonganti@101:     cingularity {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         process.queue = 'prod'
kkonganti@101:         process.memory = '10GB'
kkonganti@101:         process.cpus = 4
kkonganti@101:         singularity.enabled = true
kkonganti@101:         singularity.autoMounts = true
kkonganti@101:         docker.enabled = false
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = false
kkonganti@101:         clusterOptions = '--signal B:USR2'
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     cingularitygac {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         executor.$slurm.exitReadTimeout = 120000
kkonganti@101:         process.queue = 'centriflaken'
kkonganti@101:         process.cpus = 4
kkonganti@101:         singularity.enabled = true
kkonganti@101:         singularity.autoMounts = true
kkonganti@101:         docker.enabled = false
kkonganti@101:         params.enable_conda = false
kkonganti@101:         params.enable_module = false
kkonganti@101:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     konda {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         process.queue = 'prod'
kkonganti@101:         process.memory = '10GB'
kkonganti@101:         process.cpus = 4
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:         params.enable_conda = true
kkonganti@101:         params.enable_module = false
kkonganti@101:         clusterOptions = '--signal B:USR2'
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     kondagac {
kkonganti@101:         process.executor = 'slurm'
kkonganti@101:         executor.$slurm.exitReadTimeout = 120000
kkonganti@101:         process.queue = 'centriflaken'
kkonganti@101:         process.cpus = 4
kkonganti@101:         singularity.enabled = false
kkonganti@101:         docker.enabled = false
kkonganti@101:         params.enable_conda = true
kkonganti@101:         params.enable_module = false
kkonganti@101:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@101:     }
kkonganti@101: }