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1 process {
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2 withName: 'SPADES_ASSEMBLE' {
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3 ext.args = addParamsToSummary(
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4 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
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5 )
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6 }
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7 }
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8
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9 // Method to instantiate a new function parser
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10 // Need to refactor using ScriptParser... another day
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11 def loadThisFunction (func_file) {
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12 GroovyShell grvy_sh = new GroovyShell()
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13 def func = grvy_sh.parse(new File ( func_file ) )
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14 return func
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15 }
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16
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17 // Method to add relevant final parameters to summary log
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18 def addParamsToSummary(Map params_to_add = [:]) {
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19
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20 if (!params_to_add.isEmpty()) {
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21 def not_null_params_to_add = params_to_add.findAll {
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22 it.value.clivalue != null &&
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23 it.value.clivalue != '[:]' &&
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24 it.value.clivalue != ''
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25 }
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26
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27 params.logtheseparams += not_null_params_to_add.keySet().toList()
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28
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29 return not_null_params_to_add.collect {
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30 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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31 }.join(' ').trim()
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32 }
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33 return 1
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34 } |
