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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://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 // Default routines for MAIN
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19 include { pipelineBanner; stopNow; } from "${params.routines}"
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20
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21 // Our banner for CPIPES
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22 log.info pipelineBanner()
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23
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24 /*
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25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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26 INCLUDE ALL WORKFLOWS
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27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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28 */
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29
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30 switch ("${params.pipeline}") {
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31 case "nowayout":
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32 include { NOWAYOUT } from "${params.workflows}${params.fs}${params.pipeline}"
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33 break
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34 default:
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35 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline nowayout")
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36 }
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37
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38 /*
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39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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40 RUN ALL WORKFLOWS
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41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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42 */
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43
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44 workflow {
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45 switch ("${params.pipeline}") {
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46 case "nowayout":
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47 NOWAYOUT()
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48 break
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49 }
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50 }
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51
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52 /*
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53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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54 THE END
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55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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56 */
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