annotate 0.6.1/conf/modules.config @ 14:b0a37e88ecb5

"planemo upload"
author kkonganti
date Thu, 07 Sep 2023 10:13:31 -0400
parents 749faef1caa9
children
rev   line source
kkonganti@11 1 process {
kkonganti@11 2 publishDir = [
kkonganti@11 3 path: {
kkonganti@11 4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@11 5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@11 6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@11 7 },
kkonganti@11 8 mode: params.publish_dir_mode,
kkonganti@11 9 overwrite: params.publish_dir_overwrite,
kkonganti@11 10 saveAs: { filename -> filename =~ /^versions\.yml|genome_paths\.txt|[bettercallsalbcs].+?_mqc.*/ ? null : filename }
kkonganti@11 11 ]
kkonganti@11 12
kkonganti@11 13 errorStrategy = {
kkonganti@11 14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@11 15 }
kkonganti@11 16
kkonganti@14 17 maxRetries = 80
kkonganti@11 18
kkonganti@11 19 withLabel: 'process_femto' {
kkonganti@14 20 cpus = 2
kkonganti@11 21 }
kkonganti@11 22
kkonganti@11 23 withLabel: 'process_pico' {
kkonganti@14 24 cpus = min_cpus(2)
kkonganti@11 25 }
kkonganti@11 26
kkonganti@11 27 withLabel: 'process_nano' {
kkonganti@14 28 cpus = min_cpus(4)
kkonganti@11 29 }
kkonganti@11 30
kkonganti@11 31 withLabel: 'process_micro' {
kkonganti@14 32 cpus = min_cpus(8)
kkonganti@11 33 }
kkonganti@11 34
kkonganti@11 35 withLabel: 'process_only_mem_low' {
kkonganti@14 36 cpus = 2
kkonganti@11 37 }
kkonganti@11 38
kkonganti@11 39 withLabel: 'process_only_mem_medium' {
kkonganti@14 40 cpus = 2
kkonganti@11 41 }
kkonganti@11 42
kkonganti@11 43 withLabel: 'process_only_mem_high' {
kkonganti@14 44 cpus = 2
kkonganti@11 45 }
kkonganti@11 46
kkonganti@11 47 withLabel: 'process_low' {
kkonganti@14 48 cpus = min_cpus(8)
kkonganti@11 49 }
kkonganti@11 50
kkonganti@11 51 withLabel: 'process_medium' {
kkonganti@14 52 cpus = min_cpus(8)
kkonganti@11 53 }
kkonganti@11 54
kkonganti@11 55 withLabel: 'process_high' {
kkonganti@14 56 cpus = min_cpus(8)
kkonganti@11 57 }
kkonganti@11 58
kkonganti@11 59 withLabel: 'process_higher' {
kkonganti@14 60 cpus = min_cpus(8)
kkonganti@11 61 }
kkonganti@11 62
kkonganti@11 63 withLabel: 'process_gigantic' {
kkonganti@14 64 cpus = min_cpus(8)
kkonganti@11 65 }
kkonganti@11 66 }
kkonganti@11 67
kkonganti@11 68 if ( ( ( params.input || params.metadata ) && params.pipeline ) ||
kkonganti@11 69 ( params.pipeline.toString().equalsIgnoreCase('bettercallsal_db') && params.output) ) {
kkonganti@11 70 try {
kkonganti@11 71 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@11 72 } catch (Exception e) {
kkonganti@11 73 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@11 74 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@11 75 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@11 76 "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@11 77 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@11 78 System.exit(1)
kkonganti@11 79 }
kkonganti@11 80 }
kkonganti@11 81
kkonganti@11 82 // Function will return after sleeping for some time.
kkonganti@11 83 // Sleep time increases exponentially by task attempt.
kkonganti@11 84 def dynamic_retry(task_retry_num, factor_by) {
kkonganti@11 85 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@11 86 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@11 87 return 'retry'
kkonganti@11 88 }
kkonganti@11 89
kkonganti@11 90 // Function that will adjust the minimum number of CPU
kkonganti@11 91 // cores depending as requested by the user.
kkonganti@11 92 def min_cpus(cores) {
kkonganti@11 93 return Math.min(cores as int, "${params.max_cpus}" as int)
kkonganti@11 94 }