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kkonganti@0
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1 def fs = File.separator
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kkonganti@0
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2 def pd = "${projectDir}"
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kkonganti@0
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3
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kkonganti@0
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4 // Global parameters
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kkonganti@0
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5 includeConfig "${pd}${fs}conf${fs}manifest.config"
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kkonganti@0
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6 includeConfig "${pd}${fs}conf${fs}base.config"
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kkonganti@0
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7
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kkonganti@0
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8 // Include FASTQ config to prepare for a case when the entry point is
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kkonganti@0
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9 // FASTQ metadata CSV or FASTQ input directory
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kkonganti@0
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10 includeConfig "${pd}${fs}conf${fs}fastq.config"
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kkonganti@0
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11
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kkonganti@0
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12 if (params.pipeline != null) {
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kkonganti@0
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13 try {
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kkonganti@0
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14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
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kkonganti@0
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15 } catch (Exception e) {
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kkonganti@0
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16 System.err.println('-'.multiply(params.linewidth) + "\n" +
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kkonganti@0
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17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
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kkonganti@0
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18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
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kkonganti@0
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19 "default pipeline configuration. Please provide a pipeline \n" +
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kkonganti@0
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20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
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kkonganti@0
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21 System.exit(1)
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kkonganti@0
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22 }
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kkonganti@0
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23 }
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kkonganti@0
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24
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kkonganti@0
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25 // Include modules' conig last.
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kkonganti@0
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26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
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kkonganti@0
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27 includeConfig "${pd}${fs}conf${fs}modules.config"
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kkonganti@0
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28
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kkonganti@0
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29 // Nextflow runtime profiles
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kkonganti@0
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30 conda.cacheDir = '/nfs/home/galaxy/cfsan-centriflaken-db/kondagac_cache'
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kkonganti@0
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31 singularity.cacheDir = '/nfs/home/galaxy/cfsan-centriflaken-db/cingularitygac_cache'
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kkonganti@0
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32
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kkonganti@0
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33 profiles {
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kkonganti@0
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34 standard {
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kkonganti@0
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35 process.executor = 'local'
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kkonganti@0
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36 process.cpus = 1
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kkonganti@0
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37 params.enable_conda = false
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kkonganti@0
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38 params.enable_module = true
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kkonganti@0
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39 singularity.enabled = false
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kkonganti@0
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40 docker.enabled = false
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kkonganti@0
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41 }
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kkonganti@0
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42
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kkonganti@0
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43 raven {
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kkonganti@0
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44 process.executor = 'slurm'
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kkonganti@0
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45 process.queue = 'prod'
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kkonganti@0
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46 process.memory = '10GB'
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kkonganti@0
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47 process.cpus = 4
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kkonganti@0
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48 params.enable_conda = false
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kkonganti@0
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49 params.enable_module = true
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kkonganti@0
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50 singularity.enabled = false
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kkonganti@0
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51 docker.enabled = false
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kkonganti@0
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52 clusterOptions = '--signal B:USR2'
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kkonganti@0
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53 }
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kkonganti@0
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54
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kkonganti@0
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55 cingularity {
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kkonganti@0
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56 process.executor = 'slurm'
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kkonganti@0
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57 process.queue = 'prod'
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kkonganti@0
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58 process.memory = '10GB'
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kkonganti@0
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59 process.cpus = 4
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kkonganti@0
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60 singularity.enabled = true
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kkonganti@0
|
61 singularity.autoMounts = true
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kkonganti@0
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62 docker.enabled = false
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kkonganti@0
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63 params.enable_conda = false
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kkonganti@0
|
64 params.enable_module = false
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kkonganti@0
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65 clusterOptions = '--signal B:USR2'
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|
kkonganti@0
|
66 }
|
|
kkonganti@0
|
67
|
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kkonganti@0
|
68 cingularitygac {
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kkonganti@0
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69 process.executor = 'slurm'
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kkonganti@0
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70 executor.$slurm.exitReadTimeout = 60
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kkonganti@0
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71 process.queue = 'q16cpu'
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kkonganti@0
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72 process.cpus = 4
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|
kkonganti@0
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73 singularity.enabled = true
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kkonganti@0
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74 singularity.autoMounts = true
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kkonganti@0
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75 docker.enabled = false
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kkonganti@0
|
76 params.enable_conda = false
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|
kkonganti@0
|
77 params.enable_module = false
|
|
kkonganti@0
|
78 clusterOptions = '-n 1 --signal B:USR2'
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|
kkonganti@0
|
79 }
|
|
kkonganti@0
|
80
|
|
kkonganti@0
|
81 konda {
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|
kkonganti@0
|
82 process.executor = 'slurm'
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|
kkonganti@0
|
83 process.queue = 'prod'
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|
kkonganti@0
|
84 process.memory = '10GB'
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|
kkonganti@0
|
85 process.cpus = 4
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|
kkonganti@0
|
86 singularity.enabled = false
|
|
kkonganti@0
|
87 docker.enabled = false
|
|
kkonganti@0
|
88 params.enable_conda = true
|
|
kkonganti@0
|
89 params.enable_module = false
|
|
kkonganti@0
|
90 clusterOptions = '--signal B:USR2'
|
|
kkonganti@0
|
91 }
|
|
kkonganti@0
|
92
|
|
kkonganti@0
|
93 kondagac {
|
|
kkonganti@0
|
94 process.executor = 'slurm'
|
|
kkonganti@0
|
95 executor.$slurm.exitReadTimeout = 60
|
|
kkonganti@0
|
96 process.queue = 'q16cpu'
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|
kkonganti@0
|
97 process.cpus = 4
|
|
kkonganti@0
|
98 singularity.enabled = false
|
|
kkonganti@0
|
99 docker.enabled = false
|
|
kkonganti@0
|
100 params.enable_conda = true
|
|
kkonganti@0
|
101 params.enable_module = false
|
|
kkonganti@0
|
102 clusterOptions = '-n 1 --signal B:USR2'
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|
kkonganti@0
|
103 }
|
|
kkonganti@0
|
104 }
|
