Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/nextflow.config @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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children 6e7c58050c06
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104:17890124001d 105:52045ea4679d
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' config 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 = '/tmp'
31 singularity.cacheDir = '/tmp'
32
33 // Cleanup after running
34 // cleanup = true
35
36 profiles {
37 standard {
38 process.executor = 'local'
39 process.cpus = 1
40 params.enable_conda = false
41 params.enable_module = true
42 singularity.enabled = false
43 docker.enabled = false
44 }
45
46 stdkondagac {
47 process.executor = 'local'
48 process.cpus = 4
49 params.enable_conda = true
50 params.enable_module = false
51 singularity.enabled = false
52 docker.enabled = false
53 }
54
55 stdcingularitygac {
56 process.executor = 'local'
57 process.cpus = 4
58 params.enable_conda = false
59 params.enable_module = false
60 singularity.enabled = true
61 singularity.autoMounts = true
62 docker.enabled = false
63 }
64
65 raven {
66 process.executor = 'slurm'
67 process.queue = 'prod'
68 process.memory = '10GB'
69 process.cpus = 4
70 params.enable_conda = false
71 params.enable_module = true
72 singularity.enabled = false
73 docker.enabled = false
74 clusterOptions = '--signal B:USR2'
75 }
76
77 eprod {
78 process.executor = 'slurm'
79 process.queue = 'lowmem,midmem,bigmem'
80 process.memory = '10GB'
81 process.cpus = 4
82 params.enable_conda = false
83 params.enable_module = true
84 singularity.enabled = false
85 docker.enabled = false
86 clusterOptions = '--signal B:USR2'
87 }
88
89 eprodcingularity {
90 process.executor = 'slurm'
91 process.queue = 'lowmem,midmem,bigmem'
92 process.memory = '10GB'
93 process.cpus = 4
94 params.enable_conda = false
95 params.enable_module = false
96 singularity.enabled = true
97 singularity.autoMounts = true
98 docker.enabled = false
99 clusterOptions = '--signal B:USR2'
100 }
101
102 cingularity {
103 process.executor = 'slurm'
104 process.queue = 'prod'
105 process.memory = '10GB'
106 process.cpus = 4
107 singularity.enabled = true
108 singularity.autoMounts = true
109 docker.enabled = false
110 params.enable_conda = false
111 params.enable_module = false
112 clusterOptions = '--signal B:USR2'
113 }
114
115 cingularitygac {
116 process.executor = 'slurm'
117 executor.$slurm.exitReadTimeout = 120000
118 process.queue = 'centriflaken'
119 process.cpus = 4
120 singularity.enabled = true
121 singularity.autoMounts = true
122 docker.enabled = false
123 params.enable_conda = false
124 params.enable_module = false
125 clusterOptions = '-n 1 --signal B:USR2'
126 }
127
128 konda {
129 process.executor = 'slurm'
130 process.queue = 'prod'
131 process.memory = '10GB'
132 process.cpus = 4
133 singularity.enabled = false
134 docker.enabled = false
135 params.enable_conda = true
136 params.enable_module = false
137 clusterOptions = '--signal B:USR2'
138 }
139
140 kondagac {
141 process.executor = 'slurm'
142 executor.$slurm.exitReadTimeout = 120000
143 process.queue = 'centriflaken'
144 process.cpus = 4
145 singularity.enabled = false
146 docker.enabled = false
147 params.enable_conda = true
148 params.enable_module = false
149 clusterOptions = '-n 1 --signal B:USR2'
150 }
151
152 gxkubernetes {
153 process.executor = 'k8s'
154 k8s.namespace = 'galaxy'
155 k8s.serviceAccount = 'galaxy'
156 k8s.maxErrorRetry = 5
157 singularity.enabled = false
158 docker.enabled = true
159 params.enable_conda = false
160 params.enable_module = false
161 }
162 }