Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.7.0/conf/modules.config @ 20:133571bf891f

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author kkonganti
date Mon, 15 Jul 2024 11:42:00 -0400
parents 0e7a0053e4a6
children
rev   line source
kkonganti@17 1 process {
kkonganti@17 2 publishDir = [
kkonganti@17 3 path: {
kkonganti@17 4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@17 5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@17 6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@17 7 },
kkonganti@17 8 mode: params.publish_dir_mode,
kkonganti@17 9 overwrite: params.publish_dir_overwrite,
kkonganti@17 10 saveAs: { filename -> filename =~ /^versions\.yml|genome_paths\.txt|[bettercallsalbcs].+?_mqc.*/ ? null : filename }
kkonganti@17 11 ]
kkonganti@17 12
kkonganti@17 13 errorStrategy = {
kkonganti@17 14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@17 15 }
kkonganti@17 16
kkonganti@17 17 maxRetries = 0
kkonganti@17 18 resourceLabels = {[
kkonganti@17 19 process: task.process,
kkonganti@17 20 memoryRequested: task.memory.toString(),
kkonganti@17 21 cpusRequested: task.cpus.toString()
kkonganti@17 22 ]}
kkonganti@17 23
kkonganti@17 24 withLabel: 'process_femto' {
kkonganti@17 25 cpus = { 1 * task.attempt }
kkonganti@17 26 memory = { 1.GB * task.attempt }
kkonganti@17 27 time = { 1.h * task.attempt }
kkonganti@17 28 }
kkonganti@17 29
kkonganti@17 30 withLabel: 'process_pico' {
kkonganti@17 31 cpus = { min_cpus(2) * task.attempt }
kkonganti@17 32 memory = { 4.GB * task.attempt }
kkonganti@17 33 time = { 2.h * task.attempt }
kkonganti@17 34 }
kkonganti@17 35
kkonganti@17 36 withLabel: 'process_nano' {
kkonganti@17 37 cpus = { min_cpus(4) * task.attempt }
kkonganti@17 38 memory = { 8.GB * task.attempt }
kkonganti@17 39 time = { 4.h * task.attempt }
kkonganti@17 40 }
kkonganti@17 41
kkonganti@17 42 withLabel: 'process_micro' {
kkonganti@17 43 cpus = { min_cpus(8) * task.attempt }
kkonganti@17 44 memory = { 16.GB * task.attempt }
kkonganti@17 45 time = { 8.h * task.attempt }
kkonganti@17 46 }
kkonganti@17 47
kkonganti@17 48 withLabel: 'process_only_mem_low' {
kkonganti@17 49 cpus = { 1 * task.attempt }
kkonganti@17 50 memory = { 60.GB * task.attempt }
kkonganti@17 51 time = { 20.h * task.attempt }
kkonganti@17 52 }
kkonganti@17 53
kkonganti@17 54 withLabel: 'process_only_mem_medium' {
kkonganti@17 55 cpus = { 1 * task.attempt }
kkonganti@17 56 memory = { 100.GB * task.attempt }
kkonganti@17 57 time = { 30.h * task.attempt }
kkonganti@17 58 }
kkonganti@17 59
kkonganti@17 60 withLabel: 'process_only_mem_high' {
kkonganti@17 61 cpus = { 1 * task.attempt }
kkonganti@17 62 memory = { 120.GB * task.attempt }
kkonganti@17 63 time = { 60.h * task.attempt }
kkonganti@17 64 }
kkonganti@17 65
kkonganti@17 66 withLabel: 'process_low' {
kkonganti@17 67 cpus = { min_cpus(10) * task.attempt }
kkonganti@17 68 memory = { 60.GB * task.attempt }
kkonganti@17 69 time = { 20.h * task.attempt }
kkonganti@17 70 }
kkonganti@17 71
kkonganti@17 72 withLabel: 'process_medium' {
kkonganti@17 73 cpus = { min_cpus(10) * task.attempt }
kkonganti@17 74 memory = { 100.GB * task.attempt }
kkonganti@17 75 time = { 30.h * task.attempt }
kkonganti@17 76 }
kkonganti@17 77
kkonganti@17 78 withLabel: 'process_high' {
kkonganti@17 79 cpus = { min_cpus(10) * task.attempt }
kkonganti@17 80 memory = { 120.GB * task.attempt }
kkonganti@17 81 time = { 60.h * task.attempt }
kkonganti@17 82 }
kkonganti@17 83
kkonganti@17 84 withLabel: 'process_higher' {
kkonganti@17 85 cpus = { min_cpus(10) * task.attempt }
kkonganti@17 86 memory = { 225.GB * task.attempt }
kkonganti@17 87 time = { 60.h * task.attempt }
kkonganti@17 88 }
kkonganti@17 89
kkonganti@17 90 withLabel: 'process_gigantic' {
kkonganti@17 91 cpus = { min_cpus(10) * task.attempt }
kkonganti@17 92 memory = { 500.GB * task.attempt }
kkonganti@17 93 time = { 60.h * task.attempt }
kkonganti@17 94 }
kkonganti@17 95 }
kkonganti@17 96
kkonganti@17 97 if ( ( ( params.input || params.metadata ) && params.pipeline ) ||
kkonganti@17 98 ( params.pipeline.toString().equalsIgnoreCase('bettercallsal_db') && params.output) ) {
kkonganti@17 99 try {
kkonganti@17 100 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@17 101 } catch (Exception e) {
kkonganti@17 102 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@17 103 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@17 104 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@17 105 "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@17 106 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@17 107 System.exit(1)
kkonganti@17 108 }
kkonganti@17 109 }
kkonganti@17 110
kkonganti@17 111 // Function will return after sleeping for some time.
kkonganti@17 112 // Sleep time increases exponentially by task attempt.
kkonganti@17 113 def dynamic_retry(task_retry_num, factor_by) {
kkonganti@17 114 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@17 115 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@17 116 return 'retry'
kkonganti@17 117 }
kkonganti@17 118
kkonganti@17 119 // Function that will adjust the minimum number of CPU
kkonganti@17 120 // cores depending as requested by the user.
kkonganti@17 121 def min_cpus(cores) {
kkonganti@17 122 return Math.min(cores as int, "${params.max_cpus}" as int)
kkonganti@17 123 }