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kkonganti@0
|
1 process {
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kkonganti@0
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2 publishDir = [
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kkonganti@0
|
3 path: {
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kkonganti@0
|
4 "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
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kkonganti@0
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5 "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
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kkonganti@0
|
6 "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
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kkonganti@0
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7 },
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kkonganti@0
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8 mode: params.publish_dir_mode,
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kkonganti@0
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9 overwrite: params.publish_dir_overwrite,
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kkonganti@0
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10 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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kkonganti@0
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11 ]
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kkonganti@0
|
12
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kkonganti@0
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13 errorStrategy = {
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kkonganti@25
|
14 ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
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kkonganti@0
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15 }
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kkonganti@0
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16
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kkonganti@25
|
17 maxRetries = 21
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kkonganti@0
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18
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kkonganti@0
|
19 withLabel: 'process_femto' {
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kkonganti@17
|
20 cpus = 2
|
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kkonganti@36
|
21 memory = 64.GB
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kkonganti@0
|
22 }
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kkonganti@0
|
23
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kkonganti@0
|
24 withLabel: 'process_pico' {
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kkonganti@17
|
25 cpus = 2
|
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kkonganti@36
|
26 memory = 64.GB
|
|
kkonganti@0
|
27 }
|
|
kkonganti@0
|
28
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kkonganti@0
|
29 withLabel: 'process_nano' {
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|
kkonganti@17
|
30 cpus = 4
|
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kkonganti@36
|
31 memory = 64.GB
|
|
kkonganti@0
|
32 }
|
|
kkonganti@0
|
33
|
|
kkonganti@0
|
34 withLabel: 'process_micro' {
|
|
kkonganti@17
|
35 cpus = 8
|
|
kkonganti@36
|
36 memory = 64.GB
|
|
kkonganti@0
|
37 }
|
|
kkonganti@0
|
38
|
|
kkonganti@0
|
39 withLabel: 'process_only_mem_low' {
|
|
kkonganti@17
|
40 cpus = 2
|
|
kkonganti@36
|
41 memory = 64.GB
|
|
kkonganti@0
|
42 }
|
|
kkonganti@0
|
43
|
|
kkonganti@0
|
44 withLabel: 'process_only_mem_medium' {
|
|
kkonganti@17
|
45 cpus = 2
|
|
kkonganti@36
|
46 memory = 64.GB
|
|
kkonganti@0
|
47 }
|
|
kkonganti@0
|
48
|
|
kkonganti@0
|
49 withLabel: 'process_only_mem_high' {
|
|
kkonganti@17
|
50 cpus = 2
|
|
kkonganti@36
|
51 memory = 64.GB
|
|
kkonganti@0
|
52 }
|
|
kkonganti@0
|
53
|
|
kkonganti@0
|
54 withLabel: 'process_low' {
|
|
kkonganti@17
|
55 cpus = 8
|
|
kkonganti@36
|
56 memory = 64.GB
|
|
kkonganti@0
|
57 }
|
|
kkonganti@0
|
58
|
|
kkonganti@0
|
59 withLabel: 'process_medium' {
|
|
kkonganti@17
|
60 cpus = 8
|
|
kkonganti@36
|
61 memory = 64.GB
|
|
kkonganti@0
|
62 }
|
|
kkonganti@0
|
63
|
|
kkonganti@0
|
64 withLabel: 'process_high' {
|
|
kkonganti@17
|
65 cpus = 8
|
|
kkonganti@36
|
66 memory = 64.GB
|
|
kkonganti@0
|
67 }
|
|
kkonganti@0
|
68
|
|
kkonganti@0
|
69 withLabel: 'process_higher' {
|
|
kkonganti@17
|
70 cpus = 8
|
|
kkonganti@36
|
71 memory = 64.GB
|
|
kkonganti@0
|
72 }
|
|
kkonganti@0
|
73
|
|
kkonganti@0
|
74 withLabel: 'process_gigantic' {
|
|
kkonganti@17
|
75 cpus = 8
|
|
kkonganti@36
|
76 memory = 64.GB
|
|
kkonganti@0
|
77 }
|
|
kkonganti@0
|
78 }
|
|
kkonganti@0
|
79
|
|
kkonganti@0
|
80 if ( (params.input || params.metadata ) && params.pipeline ) {
|
|
kkonganti@0
|
81 try {
|
|
kkonganti@0
|
82 includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
|
|
kkonganti@0
|
83 } catch (Exception e) {
|
|
kkonganti@0
|
84 System.err.println('-'.multiply(params.linewidth) + "\n" +
|
|
kkonganti@0
|
85 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
|
|
kkonganti@0
|
86 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
|
|
kkonganti@0
|
87 "default pipeline's process configuration. Please provide a pipeline \n" +
|
|
kkonganti@0
|
88 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
|
|
kkonganti@0
|
89 System.exit(1)
|
|
kkonganti@0
|
90 }
|
|
kkonganti@0
|
91 }
|
|
kkonganti@0
|
92
|
|
kkonganti@0
|
93 // Function will return after sleeping for some time.
|
|
kkonganti@0
|
94 // Sleep time increases exponentially by tast attempt.
|
|
kkonganti@0
|
95 def dynamic_retry(task_retry_num, factor_by) {
|
|
kkonganti@0
|
96 println tas
|
|
kkonganti@0
|
97 sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
|
|
kkonganti@0
|
98 return 'retry'
|
|
kkonganti@0
|
99 } |
