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