annotate 0.4.0/conf/modules.config @ 101:ce6d9548fe89

"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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rev   line source
kkonganti@101 1 process {
kkonganti@101 2 publishDir = [
kkonganti@101 3 path: {
kkonganti@101 4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
kkonganti@101 5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
kkonganti@101 6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
kkonganti@101 7 },
kkonganti@101 8 mode: params.publish_dir_mode,
kkonganti@101 9 overwrite: params.publish_dir_overwrite,
kkonganti@101 10 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
kkonganti@101 11 ]
kkonganti@101 12
kkonganti@101 13 errorStrategy = {
kkonganti@101 14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
kkonganti@101 15 }
kkonganti@101 16
kkonganti@101 17 maxRetries = 80
kkonganti@101 18
kkonganti@101 19 withLabel: 'process_femto' {
kkonganti@101 20 cpus = 2
kkonganti@101 21 }
kkonganti@101 22
kkonganti@101 23 withLabel: 'process_pico' {
kkonganti@101 24 cpus = 2
kkonganti@101 25 }
kkonganti@101 26
kkonganti@101 27 withLabel: 'process_nano' {
kkonganti@101 28 cpus = 4
kkonganti@101 29 }
kkonganti@101 30
kkonganti@101 31 withLabel: 'process_micro' {
kkonganti@101 32 cpus = 8
kkonganti@101 33 }
kkonganti@101 34
kkonganti@101 35 withLabel: 'process_only_mem_low' {
kkonganti@101 36 cpus = 2
kkonganti@101 37 }
kkonganti@101 38
kkonganti@101 39 withLabel: 'process_only_mem_medium' {
kkonganti@101 40 cpus = 2
kkonganti@101 41 }
kkonganti@101 42
kkonganti@101 43 withLabel: 'process_only_mem_high' {
kkonganti@101 44 cpus = 2
kkonganti@101 45 }
kkonganti@101 46
kkonganti@101 47 withLabel: 'process_low' {
kkonganti@101 48 cpus = 8
kkonganti@101 49 }
kkonganti@101 50
kkonganti@101 51 withLabel: 'process_medium' {
kkonganti@101 52 cpus = 8
kkonganti@101 53 }
kkonganti@101 54
kkonganti@101 55 withLabel: 'process_high' {
kkonganti@101 56 cpus = 8
kkonganti@101 57 }
kkonganti@101 58
kkonganti@101 59 withLabel: 'process_higher' {
kkonganti@101 60 cpus = 8
kkonganti@101 61 }
kkonganti@101 62
kkonganti@101 63 withLabel: 'process_gigantic' {
kkonganti@101 64 cpus = 8
kkonganti@101 65 }
kkonganti@101 66 }
kkonganti@101 67
kkonganti@101 68 if ( (params.input || params.metadata ) && params.pipeline ) {
kkonganti@101 69 try {
kkonganti@101 70 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
kkonganti@101 71 } catch (Exception e) {
kkonganti@101 72 System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@101 73 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@101 74 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@101 75 "default pipeline's process configuration. Please provide a pipeline \n" +
kkonganti@101 76 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@101 77 System.exit(1)
kkonganti@101 78 }
kkonganti@101 79 }
kkonganti@101 80
kkonganti@101 81 // Function will return after sleeping for some time.
kkonganti@101 82 // Sleep time increases exponentially by task attempt.
kkonganti@101 83 def dynamic_retry(task_retry_num, factor_by) {
kkonganti@101 84 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
kkonganti@101 85 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
kkonganti@101 86 return 'retry'
kkonganti@101 87 }