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1 #!/usr/bin/env nextflow
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2
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3 /*
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4 ----------------------------------------------------------------------------------------
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5 cfsan/cpipes
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6 ----------------------------------------------------------------------------------------
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7 NAME : CPIPES
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8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
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9 GITLAB : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
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10 JIRA : https://xxxxxxxxxx/jira/projects/CPIPES/
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11 CONTRIBUTORS : Kranti Konganti
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12 ----------------------------------------------------------------------------------------
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13 */
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14
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15 // Enable DSL 2
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16 nextflow.enable.dsl = 2
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17
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18 // Enable local scope of scripts inside modules' directory
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19 // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
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20 // is solved.
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21 //
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22 // nextflow.enable.moduleBinaries = true
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23
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24 // Default routines for MAIN
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25 include { pipelineBanner; stopNow; } from "${params.routines}"
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26
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27 // Our banner for CPIPES
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28 log.info pipelineBanner()
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29
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30 /*
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31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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32 INCLUDE ALL WORKFLOWS
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33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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34 */
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35
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36 switch ("${params.pipeline}") {
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37 case "bettercallsal":
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38 include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
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39 break
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40 case "bettercallsal_lr":
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41 include { BETTERCALLSAL_LR } from "${params.workflows}${params.fs}${params.pipeline}"
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42 break
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43 case "bettercallsal_db":
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44 include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
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45 break
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46 default:
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47 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
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48 }
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49
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50 /*
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51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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52 RUN ALL WORKFLOWS
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53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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54 */
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55
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56 workflow {
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57 switch ("${params.pipeline}") {
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58 case "bettercallsal":
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59 BETTERCALLSAL()
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60 break
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61 case "bettercallsal_lr":
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62 BETTERCALLSAL_LR()
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63 break
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64 case "bettercallsal_db":
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65 BETTERCALLSAL_DB()
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66 break
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67 }
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68 }
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69
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70 /*
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71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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72 THE END
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73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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74 */
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