kkonganti@17: process {
kkonganti@17:     publishDir = [
kkonganti@17:         path: { 
kkonganti@17:             "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@17:                 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@17:                 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@17:         },
kkonganti@17:         mode: params.publish_dir_mode,
kkonganti@17:         overwrite: params.publish_dir_overwrite,
kkonganti@17:         saveAs: { filename -> filename =~ /^versions\.yml|genome_paths\.txt|[bettercallsalbcs].+?_mqc.*/ ? null : filename }
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     errorStrategy = {
kkonganti@17:         ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     maxRetries = 0
kkonganti@17:     resourceLabels = {[
kkonganti@17:         process: task.process,
kkonganti@17:         memoryRequested: task.memory.toString(),
kkonganti@17:         cpusRequested: task.cpus.toString()
kkonganti@17:     ]}
kkonganti@17: 
kkonganti@17:     withLabel: 'process_femto' {
kkonganti@17:         cpus = { 1 * task.attempt }
kkonganti@17:         memory = { 1.GB * task.attempt }
kkonganti@17:         time = { 1.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_pico' {
kkonganti@17:         cpus = { min_cpus(2) * task.attempt }
kkonganti@17:         memory = { 4.GB * task.attempt }
kkonganti@17:         time = { 2.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_nano' {
kkonganti@17:         cpus = { min_cpus(4) * task.attempt }
kkonganti@17:         memory = { 8.GB * task.attempt }
kkonganti@17:         time = { 4.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_micro' {
kkonganti@17:         cpus = { min_cpus(8) * task.attempt }
kkonganti@17:         memory = { 16.GB * task.attempt }
kkonganti@17:         time = { 8.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_only_mem_low' {
kkonganti@17:         cpus = { 1 * task.attempt }
kkonganti@17:         memory = { 60.GB * task.attempt }
kkonganti@17:         time = { 20.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_only_mem_medium' {
kkonganti@17:         cpus = { 1 * task.attempt }
kkonganti@17:         memory = { 100.GB * task.attempt }
kkonganti@17:         time = { 30.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_only_mem_high' {
kkonganti@17:         cpus = { 1 * task.attempt }
kkonganti@17:         memory = { 120.GB * task.attempt }
kkonganti@17:         time = { 60.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_low' {
kkonganti@17:         cpus = { min_cpus(10) * task.attempt }
kkonganti@17:         memory = { 60.GB * task.attempt }
kkonganti@17:         time = { 20.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_medium' {
kkonganti@17:         cpus = { min_cpus(10) * task.attempt }
kkonganti@17:         memory = { 100.GB * task.attempt }
kkonganti@17:         time = { 30.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_high' {
kkonganti@17:         cpus = { min_cpus(10) * task.attempt }
kkonganti@17:         memory = { 120.GB * task.attempt }
kkonganti@17:         time = { 60.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_higher' {
kkonganti@17:         cpus = { min_cpus(10) * task.attempt }
kkonganti@17:         memory = { 225.GB * task.attempt }
kkonganti@17:         time = { 60.h * task.attempt }
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     withLabel: 'process_gigantic' {
kkonganti@17:         cpus = { min_cpus(10) * task.attempt }
kkonganti@17:         memory = { 500.GB * task.attempt }
kkonganti@17:         time = { 60.h * task.attempt }
kkonganti@17:     }
kkonganti@17: }
kkonganti@17: 
kkonganti@17: if ( ( ( params.input || params.metadata ) && params.pipeline ) ||
kkonganti@17:     ( params.pipeline.toString().equalsIgnoreCase('bettercallsal_db') && params.output) ) {
kkonganti@17:     try {
kkonganti@17:         includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@17:     } catch (Exception e) {
kkonganti@17:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@17:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@17:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@17:             "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@17:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@17:         System.exit(1)
kkonganti@17:     }
kkonganti@17: }
kkonganti@17: 
kkonganti@17: // Function will return after sleeping for some time. 
kkonganti@17: // Sleep time increases exponentially by task attempt.
kkonganti@17: def dynamic_retry(task_retry_num, factor_by) {
kkonganti@17:     // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@17:     sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@17:     return 'retry'
kkonganti@17: }
kkonganti@17: 
kkonganti@17: // Function that will adjust the minimum number of CPU
kkonganti@17: // cores depending as requested by the user.
kkonganti@17: def min_cpus(cores) {
kkonganti@17:     return Math.min(cores as int, "${params.max_cpus}" as int)
kkonganti@17: }