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