|
kkonganti@0
|
1 def fs = File.separator
|
|
kkonganti@0
|
2 def pd = "${projectDir}"
|
|
kkonganti@0
|
3
|
|
kkonganti@0
|
4 // Global parameters
|
|
kkonganti@0
|
5 includeConfig "${pd}${fs}conf${fs}manifest.config"
|
|
kkonganti@0
|
6 includeConfig "${pd}${fs}conf${fs}base.config"
|
|
kkonganti@0
|
7
|
|
kkonganti@0
|
8 // Include FASTQ config to prepare for a case when the entry point is
|
|
kkonganti@0
|
9 // FASTQ metadata CSV or FASTQ input directory
|
|
kkonganti@0
|
10 includeConfig "${pd}${fs}conf${fs}fastq.config"
|
|
kkonganti@0
|
11
|
|
kkonganti@0
|
12 if (params.pipeline != null) {
|
|
kkonganti@0
|
13 try {
|
|
kkonganti@0
|
14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
|
|
kkonganti@0
|
15 } catch (Exception e) {
|
|
kkonganti@0
|
16 System.err.println('-'.multiply(params.linewidth) + "\n" +
|
|
kkonganti@0
|
17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
|
|
kkonganti@0
|
18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
|
|
kkonganti@0
|
19 "default pipeline configuration. Please provide a pipeline \n" +
|
|
kkonganti@0
|
20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
|
|
kkonganti@0
|
21 System.exit(1)
|
|
kkonganti@0
|
22 }
|
|
kkonganti@0
|
23 }
|
|
kkonganti@0
|
24
|
|
kkonganti@0
|
25 // Include modules' conig last.
|
|
kkonganti@0
|
26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
|
|
kkonganti@0
|
27 includeConfig "${pd}${fs}conf${fs}modules.config"
|
|
kkonganti@0
|
28
|
|
kkonganti@0
|
29 // Nextflow runtime profiles
|
|
kkonganti@34
|
30 conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
|
|
kkonganti@34
|
31 singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
|
|
kkonganti@0
|
32
|
|
kkonganti@0
|
33 profiles {
|
|
kkonganti@0
|
34 standard {
|
|
kkonganti@0
|
35 process.executor = 'local'
|
|
kkonganti@0
|
36 process.cpus = 1
|
|
kkonganti@0
|
37 params.enable_conda = false
|
|
kkonganti@0
|
38 params.enable_module = true
|
|
kkonganti@0
|
39 singularity.enabled = false
|
|
kkonganti@0
|
40 docker.enabled = false
|
|
kkonganti@0
|
41 }
|
|
kkonganti@0
|
42
|
|
kkonganti@7
|
43 stdkondagac {
|
|
kkonganti@7
|
44 process.executor = 'local'
|
|
kkonganti@7
|
45 process.cpus = 4
|
|
kkonganti@7
|
46 params.enable_conda = true
|
|
kkonganti@7
|
47 params.enable_module = false
|
|
kkonganti@7
|
48 singularity.enabled = false
|
|
kkonganti@7
|
49 docker.enabled = false
|
|
kkonganti@7
|
50 }
|
|
kkonganti@7
|
51
|
|
kkonganti@7
|
52 stdcingularitygac {
|
|
kkonganti@7
|
53 process.executor = 'local'
|
|
kkonganti@7
|
54 process.cpus = 4
|
|
kkonganti@7
|
55 params.enable_conda = false
|
|
kkonganti@7
|
56 params.enable_module = false
|
|
kkonganti@7
|
57 singularity.enabled = true
|
|
kkonganti@7
|
58 docker.enabled = false
|
|
kkonganti@7
|
59 }
|
|
kkonganti@7
|
60
|
|
kkonganti@0
|
61 raven {
|
|
kkonganti@0
|
62 process.executor = 'slurm'
|
|
kkonganti@0
|
63 process.queue = 'prod'
|
|
kkonganti@0
|
64 process.memory = '10GB'
|
|
kkonganti@0
|
65 process.cpus = 4
|
|
kkonganti@0
|
66 params.enable_conda = false
|
|
kkonganti@0
|
67 params.enable_module = true
|
|
kkonganti@0
|
68 singularity.enabled = false
|
|
kkonganti@0
|
69 docker.enabled = false
|
|
kkonganti@0
|
70 clusterOptions = '--signal B:USR2'
|
|
kkonganti@0
|
71 }
|
|
kkonganti@0
|
72
|
|
kkonganti@0
|
73 cingularity {
|
|
kkonganti@0
|
74 process.executor = 'slurm'
|
|
kkonganti@0
|
75 process.queue = 'prod'
|
|
kkonganti@0
|
76 process.memory = '10GB'
|
|
kkonganti@0
|
77 process.cpus = 4
|
|
kkonganti@0
|
78 singularity.enabled = true
|
|
kkonganti@0
|
79 singularity.autoMounts = true
|
|
kkonganti@0
|
80 docker.enabled = false
|
|
kkonganti@0
|
81 params.enable_conda = false
|
|
kkonganti@0
|
82 params.enable_module = false
|
|
kkonganti@0
|
83 clusterOptions = '--signal B:USR2'
|
|
kkonganti@0
|
84 }
|
|
kkonganti@0
|
85
|
|
kkonganti@0
|
86 cingularitygac {
|
|
kkonganti@0
|
87 process.executor = 'slurm'
|
|
kkonganti@7
|
88 executor.$slurm.exitReadTimeout = 60000
|
|
kkonganti@17
|
89 process.queue = 'q8cpu'
|
|
kkonganti@0
|
90 process.cpus = 4
|
|
kkonganti@0
|
91 singularity.enabled = true
|
|
kkonganti@0
|
92 singularity.autoMounts = true
|
|
kkonganti@0
|
93 docker.enabled = false
|
|
kkonganti@0
|
94 params.enable_conda = false
|
|
kkonganti@0
|
95 params.enable_module = false
|
|
kkonganti@0
|
96 clusterOptions = '-n 1 --signal B:USR2'
|
|
kkonganti@0
|
97 }
|
|
kkonganti@0
|
98
|
|
kkonganti@0
|
99 konda {
|
|
kkonganti@0
|
100 process.executor = 'slurm'
|
|
kkonganti@0
|
101 process.queue = 'prod'
|
|
kkonganti@0
|
102 process.memory = '10GB'
|
|
kkonganti@0
|
103 process.cpus = 4
|
|
kkonganti@0
|
104 singularity.enabled = false
|
|
kkonganti@0
|
105 docker.enabled = false
|
|
kkonganti@0
|
106 params.enable_conda = true
|
|
kkonganti@0
|
107 params.enable_module = false
|
|
kkonganti@0
|
108 clusterOptions = '--signal B:USR2'
|
|
kkonganti@0
|
109 }
|
|
kkonganti@0
|
110
|
|
kkonganti@0
|
111 kondagac {
|
|
kkonganti@0
|
112 process.executor = 'slurm'
|
|
kkonganti@7
|
113 executor.$slurm.exitReadTimeout = 60000
|
|
kkonganti@17
|
114 process.queue = 'q8cpu'
|
|
kkonganti@0
|
115 process.cpus = 4
|
|
kkonganti@0
|
116 singularity.enabled = false
|
|
kkonganti@0
|
117 docker.enabled = false
|
|
kkonganti@0
|
118 params.enable_conda = true
|
|
kkonganti@0
|
119 params.enable_module = false
|
|
kkonganti@0
|
120 clusterOptions = '-n 1 --signal B:USR2'
|
|
kkonganti@0
|
121 }
|
|
kkonganti@0
|
122 }
|
