Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/conf/modules.config @ 0:0a8dda29956e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0a8dda29956e
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 = 80
18 resourceLabels = {[
19 process: task.process,
20 memoryRequested: task.memory.toString(),
21 cpusRequested: task.cpus.toString()
22 ]}
23
24 withLabel: 'process_femto' {
25 cpus = min_cpus(2)
26 }
27
28 withLabel: 'process_pico' {
29 cpus = min_cpus(2)
30 }
31
32 withLabel: 'process_nano' {
33 cpus = min_cpus(4)
34 }
35
36 withLabel: 'process_micro' {
37 cpus = min_cpus(8)
38 }
39
40 withLabel: 'process_only_mem_low' {
41 cpus = min_cpus(2)
42 }
43
44 withLabel: 'process_only_mem_medium' {
45 cpus = min_cpus(2)
46 }
47
48 withLabel: 'process_only_mem_high' {
49 cpus = min_cpus(2)
50 }
51
52 withLabel: 'process_low' {
53 cpus = min_cpus(8)
54 }
55
56 withLabel: 'process_medium' {
57 cpus = min_cpus(8)
58 }
59
60 withLabel: 'process_high' {
61 cpus = min_cpus(8)
62 }
63
64 withLabel: 'process_higher' {
65 cpus = min_cpus(8)
66 }
67
68 withLabel: 'process_gigantic' {
69 cpus = min_cpus(8)
70 }
71 }
72
73 if ( ( ( params.input || params.metadata ) && params.pipeline ) ||
74 ( params.pipeline.toString().equalsIgnoreCase('bettercallsal_db') && params.output) ) {
75 try {
76 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
77 } catch (Exception e) {
78 System.err.println('-'.multiply(params.linewidth) + "\n" +
79 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
80 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
81 "default pipeline's process configuration. Please provide a pipeline \n" +
82 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
83 System.exit(1)
84 }
85 }
86
87 // Function will return after sleeping for some time.
88 // Sleep time increases exponentially by task attempt.
89 def dynamic_retry(task_retry_num, factor_by) {
90 // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
91 sleep(Math.pow(1.27, task_retry_num.toInteger()) as long)
92 return 'retry'
93 }
94
95 // Function that will adjust the minimum number of CPU
96 // cores depending as requested by the user.
97 def min_cpus(cores) {
98 return Math.min(cores as int, "${params.max_cpus}" as int)
99 }