kkonganti@105: def fs = File.separator
kkonganti@105: def pd = "${projectDir}"
kkonganti@105: 
kkonganti@105: // Global parameters
kkonganti@105: includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@105: includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@105: 
kkonganti@105: // Include FASTQ config to prepare for a case when the entry point is 
kkonganti@105: // FASTQ metadata CSV or FASTQ input directory
kkonganti@105: includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@105: 
kkonganti@105: if (params.pipeline != null) {
kkonganti@105:     try {
kkonganti@105:         includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@105:     } catch (Exception e) {
kkonganti@105:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@105:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@105:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@105:             "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@105:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@105:         System.exit(1)
kkonganti@105:     }
kkonganti@105: }
kkonganti@105: 
kkonganti@105: // Include modules' config last.
kkonganti@105: includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@105: includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@105: 
kkonganti@105: // Nextflow runtime profiles
kkonganti@105: conda.cacheDir = '/tmp'
kkonganti@105: singularity.cacheDir = '/tmp'
kkonganti@105: 
kkonganti@105: // Cleanup after running
kkonganti@117: cleanup = true
kkonganti@105: 
kkonganti@105: profiles {
kkonganti@105:     standard {
kkonganti@105:         process.executor = 'local'
kkonganti@105:         process.cpus = 1
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = true
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     stdkondagac {
kkonganti@105:         process.executor = 'local'
kkonganti@105:         process.cpus = 4
kkonganti@105:         params.enable_conda = true
kkonganti@105:         params.enable_module = false
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     stdcingularitygac {
kkonganti@105:         process.executor = 'local'
kkonganti@105:         process.cpus = 4
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = false
kkonganti@105:         singularity.enabled = true
kkonganti@105:         singularity.autoMounts = true
kkonganti@105:         docker.enabled = false
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     raven {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         process.queue = 'prod'
kkonganti@105:         process.memory = '10GB'
kkonganti@105:         process.cpus = 4
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = true
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:         clusterOptions = '--signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     eprod {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         process.queue = 'lowmem,midmem,bigmem'
kkonganti@105:         process.memory = '10GB'
kkonganti@105:         process.cpus = 4
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = true
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:         clusterOptions = '--signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     eprodcingularity {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         process.queue = 'lowmem,midmem,bigmem'
kkonganti@105:         process.memory = '10GB'
kkonganti@105:         process.cpus = 4
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = false
kkonganti@105:         singularity.enabled = true
kkonganti@105:         singularity.autoMounts = true
kkonganti@105:         docker.enabled = false
kkonganti@105:         clusterOptions = '--signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     cingularity {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         process.queue = 'prod'
kkonganti@105:         process.memory = '10GB'
kkonganti@105:         process.cpus = 4
kkonganti@105:         singularity.enabled = true
kkonganti@105:         singularity.autoMounts = true
kkonganti@105:         docker.enabled = false
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = false
kkonganti@105:         clusterOptions = '--signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     cingularitygac {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         executor.$slurm.exitReadTimeout = 120000
kkonganti@105:         process.queue = 'centriflaken'
kkonganti@105:         process.cpus = 4
kkonganti@105:         singularity.enabled = true
kkonganti@105:         singularity.autoMounts = true
kkonganti@105:         docker.enabled = false
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = false
kkonganti@105:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     konda {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         process.queue = 'prod'
kkonganti@105:         process.memory = '10GB'
kkonganti@105:         process.cpus = 4
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:         params.enable_conda = true
kkonganti@105:         params.enable_module = false
kkonganti@105:         clusterOptions = '--signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     kondagac {
kkonganti@105:         process.executor = 'slurm'
kkonganti@105:         executor.$slurm.exitReadTimeout = 120000
kkonganti@105:         process.queue = 'centriflaken'
kkonganti@105:         process.cpus = 4
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = false
kkonganti@105:         params.enable_conda = true
kkonganti@105:         params.enable_module = false
kkonganti@105:         clusterOptions = '-n 1 --signal B:USR2'
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     gxkubernetes {
kkonganti@105:         process.executor = 'k8s'
kkonganti@105:         k8s.namespace = 'galaxy'
kkonganti@113:         k8s.serviceAccount = 'default'
kkonganti@116:         k8s.maxErrorRetry = 3
kkonganti@120:         k8s.pod = [
kkonganti@120:             [volumeClaim: 's3-centriflaken-claim', mountPath: '/galaxy/cfsan-centriflaken-db', [subPath: '/galaxy/cfsan-centriflaken-db']],
kkonganti@120:             [volumeClaim: 's3-nextflow-claim', mountPath: '/galaxy/nf-work-dirs', [subPath: '/galaxy/nf-work-dirs']]
kkonganti@120:         ]
kkonganti@105:         singularity.enabled = false
kkonganti@105:         docker.enabled = true
kkonganti@105:         params.enable_conda = false
kkonganti@105:         params.enable_module = false
kkonganti@105:     }
kkonganti@105: }