Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/nextflow.config @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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children 17890124001d
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100:9d9537c907bd 101:ce6d9548fe89
1 def fs = File.separator
2 def pd = "${projectDir}"
3
4 // Global parameters
5 includeConfig "${pd}${fs}conf${fs}manifest.config"
6 includeConfig "${pd}${fs}conf${fs}base.config"
7
8 // Include FASTQ config to prepare for a case when the entry point is
9 // FASTQ metadata CSV or FASTQ input directory
10 includeConfig "${pd}${fs}conf${fs}fastq.config"
11
12 if (params.pipeline != null) {
13 try {
14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
15 } catch (Exception e) {
16 System.err.println('-'.multiply(params.linewidth) + "\n" +
17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
19 "default pipeline configuration. Please provide a pipeline \n" +
20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
21 System.exit(1)
22 }
23 }
24
25 // Include modules' conig last.
26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
27 includeConfig "${pd}${fs}conf${fs}modules.config"
28
29 // Nextflow runtime profiles
30 conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
31 singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
32
33 profiles {
34 standard {
35 process.executor = 'local'
36 process.cpus = 1
37 params.enable_conda = false
38 params.enable_module = true
39 singularity.enabled = false
40 docker.enabled = false
41 }
42
43 stdkondagac {
44 process.executor = 'local'
45 process.cpus = 4
46 params.enable_conda = true
47 params.enable_module = false
48 singularity.enabled = false
49 docker.enabled = false
50 }
51
52 stdcingularitygac {
53 process.executor = 'local'
54 process.cpus = 4
55 params.enable_conda = false
56 params.enable_module = false
57 singularity.enabled = true
58 docker.enabled = false
59 }
60
61 raven {
62 process.executor = 'slurm'
63 process.queue = 'prod'
64 process.memory = '10GB'
65 process.cpus = 4
66 params.enable_conda = false
67 params.enable_module = true
68 singularity.enabled = false
69 docker.enabled = false
70 clusterOptions = '--signal B:USR2'
71 }
72
73 eprod {
74 process.executor = 'slurm'
75 process.queue = 'lowmem,midmem,bigmem'
76 process.memory = '10GB'
77 process.cpus = 4
78 params.enable_conda = false
79 params.enable_module = true
80 singularity.enabled = false
81 docker.enabled = false
82 clusterOptions = '--signal B:USR2'
83 }
84
85 cingularity {
86 process.executor = 'slurm'
87 process.queue = 'prod'
88 process.memory = '10GB'
89 process.cpus = 4
90 singularity.enabled = true
91 singularity.autoMounts = true
92 docker.enabled = false
93 params.enable_conda = false
94 params.enable_module = false
95 clusterOptions = '--signal B:USR2'
96 }
97
98 cingularitygac {
99 process.executor = 'slurm'
100 executor.$slurm.exitReadTimeout = 120000
101 process.queue = 'centriflaken'
102 process.cpus = 4
103 singularity.enabled = true
104 singularity.autoMounts = true
105 docker.enabled = false
106 params.enable_conda = false
107 params.enable_module = false
108 clusterOptions = '-n 1 --signal B:USR2'
109 }
110
111 konda {
112 process.executor = 'slurm'
113 process.queue = 'prod'
114 process.memory = '10GB'
115 process.cpus = 4
116 singularity.enabled = false
117 docker.enabled = false
118 params.enable_conda = true
119 params.enable_module = false
120 clusterOptions = '--signal B:USR2'
121 }
122
123 kondagac {
124 process.executor = 'slurm'
125 executor.$slurm.exitReadTimeout = 120000
126 process.queue = 'centriflaken'
127 process.cpus = 4
128 singularity.enabled = false
129 docker.enabled = false
130 params.enable_conda = true
131 params.enable_module = false
132 clusterOptions = '-n 1 --signal B:USR2'
133 }
134 }