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1 // Main driver script
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2 manifest.mainScript = 'cpipes'
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3
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4 def fs = File.separator
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5 def pd = "${projectDir}"
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6
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7 // Global parameters
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8 includeConfig "${pd}${fs}conf${fs}manifest.config"
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9 includeConfig "${pd}${fs}conf${fs}base.config"
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10
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11 // Include FASTQ config to prepare for a case when the entry point is
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12 // FASTQ metadata CSV or FASTQ input directory
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13 includeConfig "${pd}${fs}conf${fs}fastq.config"
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14
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15 if (params.pipeline != null) {
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16 try {
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17 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
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18 } catch (Exception e) {
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19 System.err.println('-'.multiply(params.linewidth) + "\n" +
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20 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
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21 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
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22 "default pipeline configuration. Please provide a pipeline \n" +
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23 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
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24 System.exit(1)
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25 }
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26 }
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27
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28 // Include modules' config last.
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29 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
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30 includeConfig "${pd}${fs}conf${fs}modules.config"
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31
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32 // Nextflow runtime profiles
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33 conda.cacheDir = "${pd}${fs}kondagac_cache"
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34 singularity.cacheDir = "${pd}${fs}cingularitygac_cache"
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35
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36 // Clean up after successfull run
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37 // cleanup = true
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38
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39 profiles {
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40 includeConfig "${pd}${fs}conf${fs}computeinfra.config"
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41 }
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