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0
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1 process {
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2 if (params.dpubmlstpy_run) {
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3 withName: 'DOWNLOAD_PUBMLST_SCHEME' {
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4 ext.args = addParamsToSummary(
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5 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
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6 )
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7 }
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8 }
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9
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10 if (params.checkm2predict_run) {
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11 withName: 'CHECKM2_PREDICT' {
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12 ext.args = addParamsToSummary(
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13 loadThisFunction("${params.toolshelp}${params.fs}checkm2predict.nf").checkm2predictHelp(params).helpparams
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14 )
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15 }
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16 }
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17
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18 if (params.guncrun_run) {
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19 withName: 'GUNC_RUN' {
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20 ext.args = addParamsToSummary(
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21 loadThisFunction("${params.toolshelp}${params.fs}guncrun.nf").guncrunHelp(params).helpparams
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22 )
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23 }
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24 }
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25
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26 if (params.mlst_run) {
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27 withName: 'MLST' {
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28 ext.args = addParamsToSummary(
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29 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
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30 )
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31 }
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32 }
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33
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34 if (params.mashsketch_run) {
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35 withName: 'MASH_SKETCH' {
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36 ext.args = addParamsToSummary(
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37 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
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38 )
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39 }
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40 }
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41 }
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42
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43 // Method to instantiate a new function parser
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44 // Need to refactor using ScriptParser... another day
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45 def loadThisFunction (func_file) {
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46 GroovyShell grvy_sh = new GroovyShell()
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47 def func = grvy_sh.parse(new File ( func_file ) )
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48 return func
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49 }
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50
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51 // Method to add relevant final parameters to summary log
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52 def addParamsToSummary(Map params_to_add = [:]) {
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53
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54 if (!params_to_add.isEmpty()) {
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55 def not_null_params_to_add = params_to_add.findAll {
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56 it.value.clivalue != null &&
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57 it.value.clivalue != '[:]' &&
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58 it.value.clivalue != ''
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59 }
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60
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61 params.logtheseparams += not_null_params_to_add.keySet().toList()
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62
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63 return not_null_params_to_add.collect {
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64 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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65 }.join(' ').trim()
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66 }
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67 return 1
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68 } |
