Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/conf/modules.config @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
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.equals('versions.yml') ? null : filename }
11 ]
12
13 errorStrategy = {
14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
15 }
16
17 maxRetries = 1
18
19 withLabel: 'process_femto' {
20 cpus = { 1 * task.attempt }
21 memory = { 1.GB * task.attempt }
22 time = { 1.h * task.attempt }
23 }
24
25 withLabel: 'process_pico' {
26 cpus = { 2 * task.attempt }
27 memory = { 4.GB * task.attempt }
28 time = { 2.h * task.attempt }
29 }
30
31 withLabel: 'process_nano' {
32 cpus = { 4 * task.attempt }
33 memory = { 8.GB * task.attempt }
34 time = { 4.h * task.attempt }
35 }
36
37 withLabel: 'process_micro' {
38 cpus = { 8 * task.attempt }
39 memory = { 16.GB * task.attempt }
40 time = { 8.h * task.attempt }
41 }
42
43 withLabel: 'process_only_mem_low' {
44 cpus = { 1 * task.attempt }
45 memory = { 60.GB * task.attempt }
46 time = { 20.h * task.attempt }
47 }
48
49 withLabel: 'process_only_mem_medium' {
50 cpus = { 1 * task.attempt }
51 memory = { 100.GB * task.attempt }
52 time = { 30.h * task.attempt }
53 }
54
55 withLabel: 'process_only_mem_high' {
56 cpus = { 1 * task.attempt }
57 memory = { 128.GB * task.attempt }
58 time = { 60.h * task.attempt }
59 }
60
61 withLabel: 'process_low' {
62 cpus = { 10 * task.attempt }
63 memory = { 60.GB * task.attempt }
64 time = { 20.h * task.attempt }
65 }
66
67 withLabel: 'process_medium' {
68 cpus = { 10 * task.attempt }
69 memory = { 100.GB * task.attempt }
70 time = { 30.h * task.attempt }
71 }
72
73 withLabel: 'process_high' {
74 cpus = { 10 * task.attempt }
75 memory = { 128.GB * task.attempt }
76 time = { 60.h * task.attempt }
77 }
78
79 withLabel: 'process_higher' {
80 cpus = { 10 * task.attempt }
81 memory = { 256.GB * task.attempt }
82 time = { 60.h * task.attempt }
83 }
84
85 withLabel: 'process_gigantic' {
86 cpus = { 10 * task.attempt }
87 memory = { 512.GB * task.attempt }
88 time = { 60.h * task.attempt }
89 }
90 }
91
92 if ( (params.input || params.metadata ) && params.pipeline ) {
93 try {
94 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
95 } catch (Exception e) {
96 System.err.println('-'.multiply(params.linewidth) + "\n" +
97 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
98 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
99 "default pipeline's process configuration. Please provide a pipeline \n" +
100 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
101 System.exit(1)
102 }
103 }
104
105 // Function will return after sleeping for some time.
106 // Sleep time increases exponentially by task attempt.
107 def dynamic_retry(task_retry_num, factor_by) {
108 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
109 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
110 return 'retry'
111 }