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comparison CSP2/conf/profiles.config @ 0:01431fa12065

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"planemo upload"
author rliterman
date Mon, 02 Dec 2024 10:40:55 -0500
parents
children 27af39d069b3
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-1:000000000000 0:01431fa12065
1 profiles {
2
3 standard {
4 process.executor = 'local'
5 params.cores = 1
6 params.python_module = ""
7 params.mummer_module = ""
8 params.skesa_module = ""
9 params.bedtools_module = ""
10 params.mash_module = ""
11 params.bbtools_module = ""
12 }
13
14 slurmHPC {
15 process.executor = 'slurm'
16 params.cores = 20
17 params.python_module = "/nfs/software/modules/python/3.8.1"
18 params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
19 params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
20 params.bedtools_module = "/nfs/sw/Modules/bedtools"
21 params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
22 params.mash_module = "/nfs/software/modules/mash/2.3"
23 params.trim_name = "_contigs_skesa"
24 }
25
26 slurmHPC_int {
27 process.executor = 'local'
28 params.cores = 20
29 params.python_module = "/nfs/software/modules/python/3.8.1"
30 params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
31 params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
32 params.bedtools_module = "/nfs/sw/Modules/bedtools"
33 params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
34 params.mash_module = "/nfs/software/modules/mash/2.3"
35 params.trim_name = "_contigs_skesa"
36 }
37
38 slurm_nm {
39 process.executor = 'slurm'
40 params.cores = 1
41 params.python_module = ""
42 params.mummer_module = ""
43 params.skesa_module = ""
44 params.bedtools_module = ""
45 params.bbtools_module = ""
46 params.mash_module = ""
47 params.trim_name = ""
48 }
49
50 standard_conda {
51 conda.enabled = true
52 conda.cacheDir = "${projectDir}/CSP2_env"
53 process.conda = "${projectDir}/conf/CSP2.yaml"
54
55 process.executor = 'local'
56 params.cores = 1
57 params.python_module = ""
58 params.mummer_module = ""
59 params.skesa_module = ""
60 params.bedtools_module = ""
61 params.bbtools_module = ""
62 params.mash_module = ""
63 params.trim_name = ""
64 }
65
66 slurm_conda {
67 conda.enabled = true
68 conda.cacheDir = "${projectDir}/CSP2_env"
69 process.conda = "${projectDir}/conf/CSP2.yaml"
70
71 process.executor = 'slurm'
72 params.cores = 1
73 params.python_module = ""
74 params.mummer_module = ""
75 params.skesa_module = ""
76 params.bedtools_module = ""
77 params.bbtools_module = ""
78 params.mash_module = ""
79 params.trim_name = ""
80 }
81
82 csp2_galaxy {
83 conda.enabled = true
84 conda.useMicromamba = true
85 conda.cacheDir = "${projectDir}/CSP2_env"
86 process.conda = "${projectDir}/conf/CSP2.yaml"
87
88 process.queue = 'centriflaken'
89 executor.$slurm.exitReadTimeout = 120000
90
91 process.executor = 'slurm'
92 params.cores = 8
93 params.python_module = ""
94 params.mummer_module = ""
95 params.skesa_module = ""
96 params.bedtools_module = ""
97 params.bbtools_module = ""
98 params.mash_module = ""
99 params.trim_name = ""
100 }
101 }