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kkonganti@92
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1 def fs = File.separator
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kkonganti@92
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2 def pd = "${projectDir}"
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kkonganti@92
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3
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kkonganti@92
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4 // Global parameters
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kkonganti@92
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5 includeConfig "${pd}${fs}conf${fs}manifest.config"
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kkonganti@92
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6 includeConfig "${pd}${fs}conf${fs}base.config"
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kkonganti@92
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7
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kkonganti@92
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8 // Include FASTQ config to prepare for a case when the entry point is
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kkonganti@92
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9 // FASTQ metadata CSV or FASTQ input directory
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kkonganti@92
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10 includeConfig "${pd}${fs}conf${fs}fastq.config"
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kkonganti@92
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11
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kkonganti@92
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12 if (params.pipeline != null) {
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kkonganti@92
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13 try {
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kkonganti@92
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14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
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kkonganti@92
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15 } catch (Exception e) {
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kkonganti@92
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16 System.err.println('-'.multiply(params.linewidth) + "\n" +
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kkonganti@92
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17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
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kkonganti@92
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18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
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kkonganti@92
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19 "default pipeline configuration. Please provide a pipeline \n" +
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kkonganti@92
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20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
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kkonganti@92
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21 System.exit(1)
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kkonganti@92
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22 }
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kkonganti@92
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23 }
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kkonganti@92
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24
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kkonganti@92
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25 // Include modules' conig last.
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kkonganti@92
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26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
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kkonganti@92
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27 includeConfig "${pd}${fs}conf${fs}modules.config"
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kkonganti@92
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28
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kkonganti@92
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29 // Nextflow runtime profiles
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kkonganti@97
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30 conda.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/kondagac_cache'
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kkonganti@97
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31 singularity.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/cingularitygac_cache'
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kkonganti@92
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32
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kkonganti@92
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33 profiles {
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kkonganti@92
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34 standard {
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kkonganti@92
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35 process.executor = 'local'
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kkonganti@92
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36 process.cpus = 1
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kkonganti@92
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37 params.enable_conda = false
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kkonganti@92
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38 params.enable_module = true
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kkonganti@92
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39 singularity.enabled = false
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kkonganti@92
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40 docker.enabled = false
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kkonganti@92
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41 }
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kkonganti@92
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42
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kkonganti@92
|
43 stdkondagac {
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kkonganti@92
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44 process.executor = 'local'
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kkonganti@92
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45 process.cpus = 4
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kkonganti@92
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46 params.enable_conda = true
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kkonganti@92
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47 params.enable_module = false
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kkonganti@92
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48 singularity.enabled = false
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kkonganti@92
|
49 docker.enabled = false
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kkonganti@92
|
50 }
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kkonganti@92
|
51
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kkonganti@92
|
52 stdcingularitygac {
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kkonganti@92
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53 process.executor = 'local'
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kkonganti@92
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54 process.cpus = 4
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kkonganti@92
|
55 params.enable_conda = false
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kkonganti@92
|
56 params.enable_module = false
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kkonganti@92
|
57 singularity.enabled = true
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|
kkonganti@92
|
58 docker.enabled = false
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|
kkonganti@92
|
59 }
|
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kkonganti@92
|
60
|
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kkonganti@92
|
61 raven {
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kkonganti@92
|
62 process.executor = 'slurm'
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|
kkonganti@92
|
63 process.queue = 'prod'
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kkonganti@92
|
64 process.memory = '10GB'
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|
kkonganti@92
|
65 process.cpus = 4
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|
kkonganti@92
|
66 params.enable_conda = false
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kkonganti@92
|
67 params.enable_module = true
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|
kkonganti@92
|
68 singularity.enabled = false
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kkonganti@92
|
69 docker.enabled = false
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kkonganti@92
|
70 clusterOptions = '--signal B:USR2'
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|
kkonganti@92
|
71 }
|
|
kkonganti@92
|
72
|
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kkonganti@92
|
73 cingularity {
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kkonganti@92
|
74 process.executor = 'slurm'
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|
kkonganti@92
|
75 process.queue = 'prod'
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|
kkonganti@92
|
76 process.memory = '10GB'
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|
kkonganti@92
|
77 process.cpus = 4
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|
kkonganti@92
|
78 singularity.enabled = true
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|
kkonganti@92
|
79 singularity.autoMounts = true
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|
kkonganti@92
|
80 docker.enabled = false
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|
kkonganti@92
|
81 params.enable_conda = false
|
|
kkonganti@92
|
82 params.enable_module = false
|
|
kkonganti@92
|
83 clusterOptions = '--signal B:USR2'
|
|
kkonganti@92
|
84 }
|
|
kkonganti@92
|
85
|
|
kkonganti@92
|
86 cingularitygac {
|
|
kkonganti@92
|
87 process.executor = 'slurm'
|
|
kkonganti@92
|
88 executor.$slurm.exitReadTimeout = 120000
|
|
kkonganti@92
|
89 process.queue = 'q8cpu'
|
|
kkonganti@92
|
90 process.cpus = 4
|
|
kkonganti@92
|
91 singularity.enabled = true
|
|
kkonganti@92
|
92 singularity.autoMounts = true
|
|
kkonganti@92
|
93 docker.enabled = false
|
|
kkonganti@92
|
94 params.enable_conda = false
|
|
kkonganti@92
|
95 params.enable_module = false
|
|
kkonganti@92
|
96 clusterOptions = '-n 1 --signal B:USR2'
|
|
kkonganti@92
|
97 }
|
|
kkonganti@92
|
98
|
|
kkonganti@92
|
99 konda {
|
|
kkonganti@92
|
100 process.executor = 'slurm'
|
|
kkonganti@92
|
101 process.queue = 'prod'
|
|
kkonganti@92
|
102 process.memory = '10GB'
|
|
kkonganti@92
|
103 process.cpus = 4
|
|
kkonganti@92
|
104 singularity.enabled = false
|
|
kkonganti@92
|
105 docker.enabled = false
|
|
kkonganti@92
|
106 params.enable_conda = true
|
|
kkonganti@92
|
107 params.enable_module = false
|
|
kkonganti@92
|
108 clusterOptions = '--signal B:USR2'
|
|
kkonganti@92
|
109 }
|
|
kkonganti@92
|
110
|
|
kkonganti@92
|
111 kondagac {
|
|
kkonganti@92
|
112 process.executor = 'slurm'
|
|
kkonganti@92
|
113 executor.$slurm.exitReadTimeout = 120000
|
|
kkonganti@92
|
114 process.queue = 'q8cpu'
|
|
kkonganti@92
|
115 process.cpus = 4
|
|
kkonganti@92
|
116 singularity.enabled = false
|
|
kkonganti@92
|
117 docker.enabled = false
|
|
kkonganti@92
|
118 params.enable_conda = true
|
|
kkonganti@92
|
119 params.enable_module = false
|
|
kkonganti@92
|
120 clusterOptions = '-n 1 --signal B:USR2'
|
|
kkonganti@92
|
121 }
|
|
kkonganti@92
|
122 }
|
