Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/conf/modules.config @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process {
2 publishDir = [
3 path: {
4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
7 },
8 mode: params.publish_dir_mode,
9 overwrite: params.publish_dir_overwrite,
10 saveAs: { filename -> filename =~ /^versions\.yml|genome_paths\.txt|[bettercallsalbcs].+?_mqc.*/ ? null : filename }
11 ]
12
13 errorStrategy = {
14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
15 }
16
17 maxRetries = 1
18 resourceLabels = {[
19 process: task.process,
20 memoryRequested: task.memory.toString(),
21 cpusRequested: task.cpus.toString()
22 ]}
23
24 withLabel: 'process_femto' {
25 cpus = { 1 * task.attempt }
26 memory = { 1.GB * task.attempt }
27 time = { 1.h * task.attempt }
28 }
29
30 withLabel: 'process_pico' {
31 cpus = { min_cpus(2) * task.attempt }
32 memory = { 4.GB * task.attempt }
33 time = { 2.h * task.attempt }
34 }
35
36 withLabel: 'process_nano' {
37 cpus = { min_cpus(4) * task.attempt }
38 memory = { 8.GB * task.attempt }
39 time = { 4.h * task.attempt }
40 }
41
42 withLabel: 'process_micro' {
43 cpus = { min_cpus(8) * task.attempt }
44 memory = { 16.GB * task.attempt }
45 time = { 8.h * task.attempt }
46 }
47
48 withLabel: 'process_only_mem_low' {
49 cpus = { 1 * task.attempt }
50 memory = { 60.GB * task.attempt }
51 time = { 20.h * task.attempt }
52 }
53
54 withLabel: 'process_only_mem_medium' {
55 cpus = { 1 * task.attempt }
56 memory = { 100.GB * task.attempt }
57 time = { 30.h * task.attempt }
58 }
59
60 withLabel: 'process_only_mem_high' {
61 cpus = { 1 * task.attempt }
62 memory = { 128.GB * task.attempt }
63 time = { 60.h * task.attempt }
64 }
65
66 withLabel: 'process_low' {
67 cpus = { min_cpus(10) * task.attempt }
68 memory = { 60.GB * task.attempt }
69 time = { 20.h * task.attempt }
70 }
71
72 withLabel: 'process_medium' {
73 cpus = { min_cpus(10) * task.attempt }
74 memory = { 100.GB * task.attempt }
75 time = { 30.h * task.attempt }
76 }
77
78 withLabel: 'process_high' {
79 cpus = { min_cpus(10) * task.attempt }
80 memory = { 128.GB * task.attempt }
81 time = { 60.h * task.attempt }
82 }
83
84 withLabel: 'process_higher' {
85 cpus = { min_cpus(10) * task.attempt }
86 memory = { 256.GB * task.attempt }
87 time = { 60.h * task.attempt }
88 }
89
90 withLabel: 'process_gigantic' {
91 cpus = { min_cpus(10) * task.attempt }
92 memory = { 512.GB * task.attempt }
93 time = { 60.h * task.attempt }
94 }
95 }
96
97 if ( ( ( params.input || params.metadata ) && params.pipeline ) ||
98 ( params.pipeline.toString().equalsIgnoreCase('bettercallsal_db') && params.output) ) {
99 try {
100 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
101 } catch (Exception e) {
102 System.err.println('-'.multiply(params.linewidth) + "\n" +
103 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
104 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
105 "default pipeline's process configuration. Please provide a pipeline \n" +
106 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
107 System.exit(1)
108 }
109 }
110
111 // Function will return after sleeping for some time.
112 // Sleep time increases exponentially by task attempt.
113 def dynamic_retry(task_retry_num, factor_by) {
114 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
115 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
116 return 'retry'
117 }
118
119 // Function that will adjust the minimum number of CPU
120 // cores depending as requested by the user.
121 def min_cpus(cores) {
122 return Math.min(cores as int, "${params.max_cpus}" as int)
123 }