kkonganti@130: process {
kkonganti@130:     publishDir = [
kkonganti@130:         path: { 
kkonganti@130:             "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@130:                 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@130:                 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@130:         },
kkonganti@130:         mode: params.publish_dir_mode,
kkonganti@130:         overwrite: params.publish_dir_overwrite,
kkonganti@130:         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
kkonganti@130:     ]
kkonganti@130: 
kkonganti@130:     errorStrategy = {
kkonganti@130:         ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     maxRetries = 5
kkonganti@130: 
kkonganti@130:     withLabel: 'process_femto' {
kkonganti@130:         cpus = 2
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_pico' {
kkonganti@130:         cpus = 2
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_nano' {
kkonganti@130:         cpus = 4
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_micro' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_only_mem_low' {
kkonganti@130:         cpus = 2
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_only_mem_medium' {
kkonganti@130:         cpus = 2
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_only_mem_high' {
kkonganti@130:         cpus = 2
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_low' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_medium' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_high' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_higher' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: 
kkonganti@130:     withLabel: 'process_gigantic' {
kkonganti@130:         cpus = 8
kkonganti@130:     }
kkonganti@130: }
kkonganti@130: 
kkonganti@130: if ( (params.input || params.metadata ) && params.pipeline ) {
kkonganti@130:     try {
kkonganti@130:         includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@130:     } catch (Exception e) {
kkonganti@130:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@130:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@130:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@130:             "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@130:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@130:         System.exit(1)
kkonganti@130:     }
kkonganti@130: }
kkonganti@130: 
kkonganti@130: // Function will return after sleeping for some time. 
kkonganti@130: // Sleep time increases exponentially by task attempt.
kkonganti@130: def dynamic_retry(task_retry_num, factor_by) {
kkonganti@130:     // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@130:     sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@130:     return 'retry'
kkonganti@130: }