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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-dev/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://cfsan-git.fda.gov/cfsan-dev/cpipes
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10 JIRA : https://sde.fda.gov/jira/projects/CPIPES/
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11 CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov
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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 // Default routines for MAIN
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19 include { pipelineBanner; stopNow; } from "${params.routines}"
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20
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21 // Our banner for CPIPES
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22 log.info pipelineBanner()
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23
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24 /*
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25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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26 NAMED WORKFLOW CAN BE USED TO RUN A SPECIFIC PIPELINE. THIS IS THE RECOMMENDED WAY.
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27 NEED TO FIND A BETTER SOLUTION IF WE SEE A LOT OF PIPELINES.
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28 See: https://github.com/nf-core/rnaseq/issues/619
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29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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30 */
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31
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32 switch ("${params.pipeline}") {
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33 case "nanofactory":
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34 include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
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35 break
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36 case "centriflaken":
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37 include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
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38 break
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39 case "centriflaken_hy":
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40 include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
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41 break
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42 default:
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43 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
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44 }
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45
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46 /*
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47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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48 RUN ALL WORKFLOWS
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49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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50 */
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51
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52 workflow {
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53 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
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54 // INSIDE WORKFLOW
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55 switch ("${params.pipeline}") {
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56 case "nanofactory":
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57 NANOFACTORY()
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58 break
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59 case "centriflaken":
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60 CENTRIFLAKEN()
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61 break
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62 case "centriflaken_hy":
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63 CENTRIFLAKEN_HY()
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64 break
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65 }
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66 }
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67
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68 /*
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69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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70 THE END
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71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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72 */
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