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