Mercurial > repos > kkonganti > hfp_nowayout

annotate 0.5.0/conf/modules.config @ 10:74ac6f6a9526 tip

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planemo upload
author kkonganti
date Tue, 01 Apr 2025 11:08:01 -0400
parents 97cd2f532efe
children
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kkonganti@0 1 process {
kkonganti@0 2 publishDir = [
kkonganti@0 3 path: {
kkonganti@0 4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@0 5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@0 6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@0 7 },
kkonganti@0 8 mode: params.publish_dir_mode,
kkonganti@0 9 overwrite: params.publish_dir_overwrite,
kkonganti@0 10 saveAs: { filename -> filename =~ /^versions.yml|.+?_mqc.*/ ? null : filename }
kkonganti@0 11 ]
kkonganti@0 12
kkonganti@0 13 errorStrategy = {
kkonganti@0 14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@0 15 }
kkonganti@0 16
kkonganti@0 17 maxRetries = 1
kkonganti@0 18 resourceLabels = {[
kkonganti@0 19 process: task.process,
kkonganti@0 20 memoryRequested: task.memory.toString(),
kkonganti@0 21 cpusRequested: task.cpus.toString()
kkonganti@0 22 ]}
kkonganti@0 23
kkonganti@0 24 withLabel: 'process_femto' {
kkonganti@0 25 cpus = { 1 * task.attempt }
kkonganti@0 26 memory = { 1.GB * task.attempt }
kkonganti@0 27 time = { 1.h * task.attempt }
kkonganti@0 28 }
kkonganti@0 29
kkonganti@0 30 withLabel: 'process_pico' {
kkonganti@0 31 cpus = { min_cpus(2) * task.attempt }
kkonganti@0 32 memory = { 4.GB * task.attempt }
kkonganti@0 33 time = { 2.h * task.attempt }
kkonganti@0 34 }
kkonganti@0 35
kkonganti@0 36 withLabel: 'process_nano' {
kkonganti@0 37 cpus = { min_cpus(4) * task.attempt }
kkonganti@0 38 memory = { 8.GB * task.attempt }
kkonganti@0 39 time = { 4.h * task.attempt }
kkonganti@0 40 }
kkonganti@0 41
kkonganti@0 42 withLabel: 'process_micro' {
kkonganti@0 43 cpus = { min_cpus(8) * task.attempt }
kkonganti@0 44 memory = { 16.GB * task.attempt }
kkonganti@0 45 time = { 8.h * task.attempt }
kkonganti@0 46 }
kkonganti@0 47
kkonganti@0 48 withLabel: 'process_only_mem_low' {
kkonganti@0 49 cpus = { 1 * task.attempt }
kkonganti@0 50 memory = { 60.GB * task.attempt }
kkonganti@0 51 time = { 20.h * task.attempt }
kkonganti@0 52 }
kkonganti@0 53
kkonganti@0 54 withLabel: 'process_only_mem_medium' {
kkonganti@0 55 cpus = { 1 * task.attempt }
kkonganti@0 56 memory = { 100.GB * task.attempt }
kkonganti@0 57 time = { 30.h * task.attempt }
kkonganti@0 58 }
kkonganti@0 59
kkonganti@0 60 withLabel: 'process_only_mem_high' {
kkonganti@0 61 cpus = { 1 * task.attempt }
kkonganti@0 62 memory = { 128.GB * task.attempt }
kkonganti@0 63 time = { 60.h * task.attempt }
kkonganti@0 64 }
kkonganti@0 65
kkonganti@0 66 withLabel: 'process_low' {
kkonganti@0 67 cpus = { min_cpus(10) * task.attempt }
kkonganti@0 68 memory = { 60.GB * task.attempt }
kkonganti@0 69 time = { 20.h * task.attempt }
kkonganti@0 70 }
kkonganti@0 71
kkonganti@0 72 withLabel: 'process_medium' {
kkonganti@0 73 cpus = { min_cpus(10) * task.attempt }
kkonganti@0 74 memory = { 100.GB * task.attempt }
kkonganti@0 75 time = { 30.h * task.attempt }
kkonganti@0 76 }
kkonganti@0 77
kkonganti@0 78 withLabel: 'process_high' {
kkonganti@0 79 cpus = { min_cpus(10) * task.attempt }
kkonganti@0 80 memory = { 128.GB * task.attempt }
kkonganti@0 81 time = { 60.h * task.attempt }
kkonganti@0 82 }
kkonganti@0 83
kkonganti@0 84 withLabel: 'process_higher' {
kkonganti@0 85 cpus = { min_cpus(10) * task.attempt }
kkonganti@0 86 memory = { 256.GB * task.attempt }
kkonganti@0 87 time = { 60.h * task.attempt }
kkonganti@0 88 }
kkonganti@0 89
kkonganti@0 90 withLabel: 'process_gigantic' {
kkonganti@0 91 cpus = { min_cpus(10) * task.attempt }
kkonganti@0 92 memory = { 512.GB * task.attempt }
kkonganti@0 93 time = { 60.h * task.attempt }
kkonganti@0 94 }
kkonganti@0 95 }
kkonganti@0 96
kkonganti@0 97 if ( (params.input || params.metadata ) && params.pipeline ) {
kkonganti@0 98 try {
kkonganti@0 99 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@0 100 } catch (Exception e) {
kkonganti@0 101 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@0 102 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@0 103 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@0 104 "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@0 105 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@0 106 System.exit(1)
kkonganti@0 107 }
kkonganti@0 108 }
kkonganti@0 109
kkonganti@0 110 // Function will return after sleeping for some time.
kkonganti@0 111 // Sleep time increases exponentially by task attempt.
kkonganti@0 112 def dynamic_retry(task_retry_num, factor_by) {
kkonganti@0 113 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@0 114 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@0 115 return 'retry'
kkonganti@0 116 }
kkonganti@0 117
kkonganti@0 118 // Function that will adjust the minimum number of CPU
kkonganti@0 119 // cores depending as requested by the user.
kkonganti@0 120 def min_cpus(cores) {
kkonganti@0 121 return Math.min(cores as int, "${params.max_cpus}" as int)
kkonganti@0 122 }