Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/nextflow.config @ 0:77494b0fa3c7

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"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 15:55:37 -0400
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children fc2d7be75a28
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-1:000000000000 0:77494b0fa3c7
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 = '/nfs/home/galaxy/cfsan-centriflaken-db/kondagac_cache'
31 singularity.cacheDir = '/nfs/home/galaxy/cfsan-centriflaken-db/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 raven {
44 process.executor = 'slurm'
45 process.queue = 'prod'
46 process.memory = '10GB'
47 process.cpus = 4
48 params.enable_conda = false
49 params.enable_module = true
50 singularity.enabled = false
51 docker.enabled = false
52 clusterOptions = '--signal B:USR2'
53 }
54
55 cingularity {
56 process.executor = 'slurm'
57 process.queue = 'prod'
58 process.memory = '10GB'
59 process.cpus = 4
60 singularity.enabled = true
61 singularity.autoMounts = true
62 docker.enabled = false
63 params.enable_conda = false
64 params.enable_module = false
65 clusterOptions = '--signal B:USR2'
66 }
67
68 cingularitygac {
69 process.executor = 'slurm'
70 executor.$slurm.exitReadTimeout = 60
71 process.queue = 'q16cpu'
72 process.cpus = 4
73 singularity.enabled = true
74 singularity.autoMounts = true
75 docker.enabled = false
76 params.enable_conda = false
77 params.enable_module = false
78 clusterOptions = '-n 1 --signal B:USR2'
79 }
80
81 konda {
82 process.executor = 'slurm'
83 process.queue = 'prod'
84 process.memory = '10GB'
85 process.cpus = 4
86 singularity.enabled = false
87 docker.enabled = false
88 params.enable_conda = true
89 params.enable_module = false
90 clusterOptions = '--signal B:USR2'
91 }
92
93 kondagac {
94 process.executor = 'slurm'
95 executor.$slurm.exitReadTimeout = 60
96 process.queue = 'q16cpu'
97 process.cpus = 4
98 singularity.enabled = false
99 docker.enabled = false
100 params.enable_conda = true
101 params.enable_module = false
102 clusterOptions = '-n 1 --signal B:USR2'
103 }
104 }