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0
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1 process {
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2 withName: 'SEQKIT_SEQ' {
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3 ext.args = [
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4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
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5 ].join(' ').trim()
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6 }
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7
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8 if (params.dpubmlstpy_run) {
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9 withName: 'DOWNLOAD_PUBMLST_SCHEME' {
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10 ext.args = addParamsToSummary(
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11 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
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12 )
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13 }
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14 }
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15
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16 if (params.fastp_run) {
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17 withName: 'FASTP' {
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18 ext.args = addParamsToSummary(
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19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
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20 )
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21 }
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22 }
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23
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24 if (params.mashscreen_run) {
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25 withName: 'MASH_SCREEN' {
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26 ext.args = addParamsToSummary(
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27 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
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28 )
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29 }
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30 }
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31
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32 if (params.tuspy_run) {
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33 withName: 'TOP_UNIQUE_SEROVARS' {
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34 ext.args = addParamsToSummary(
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35 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
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36 )
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37 }
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38 }
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39
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40 if (params.spades_run) {
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41 withName: 'SPADES_ASSEMBLE' {
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42 errorStrategy = 'ignore'
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43 ext.args = addParamsToSummary(
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44 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
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45 )
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46 }
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47 }
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48
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49 if (params.shovill_run) {
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50 withName: 'SHOVILL' {
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51 errorStrategy = 'ignore'
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52 ext.args = addParamsToSummary(
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53 loadThisFunction("${params.toolshelp}${params.fs}shovill.nf").shovillHelp(params).helpparams
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54 )
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55 }
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56 }
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57
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58 if (params.polypolish_run) {
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59 withName: 'POLYPOLISH' {
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60 ext.args = addParamsToSummary(
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61 loadThisFunction("${params.toolshelp}${params.fs}polypolish.nf").polypolishHelp(params).helpparams
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62 )
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63 }
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64 }
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65
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66 if (params.quast_run) {
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67 withName: 'QUAST' {
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68 ext.args = addParamsToSummary(
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69 loadThisFunction("${params.toolshelp}${params.fs}quast.nf").quastHelp(params).helpparams
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70 )
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71 }
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72 }
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73
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74 if (params.pirate_run) {
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75 withName: 'PIRATE' {
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76 ext.args = addParamsToSummary(
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77 loadThisFunction("${params.toolshelp}${params.fs}pirate.nf").pirateHelp(params).helpparams
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78 )
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79 }
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80 }
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81
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82 if (params.prodka_run) {
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83 withName: 'PRODIGAL' {
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84 ext.args = addParamsToSummary(
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85 loadThisFunction("${params.toolshelp}${params.fs}prodigal.nf").prodigalHelp(params).helpparams
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86 )
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87 }
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88
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89 withName: 'PROKKA' {
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90 ext.args = addParamsToSummary(
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91 loadThisFunction("${params.toolshelp}${params.fs}prokka.nf").prokkaHelp(params).helpparams
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92 )
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93 }
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94 }
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95
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96 if (params.mlst_run) {
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97 withName: 'MLST' {
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98 ext.args = addParamsToSummary(
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99 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
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100 )
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101 }
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102 }
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103
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104 if (params.abricate_run) {
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105 withName: 'ABRICATE_RUN' {
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106 ext.args = addParamsToSummary(
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107 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
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108 )
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109 }
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110 }
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111
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112 if (params.mashtree_run) {
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113 withName: 'MASHTREE' {
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114 ext.args = addParamsToSummary(
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115 loadThisFunction("${params.toolshelp}${params.fs}mashtree.nf").mashtreeHelp(params).helpparams
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116 )
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117 }
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118 }
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119
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120 if (params.upload_microreact) {
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121 withName: 'UPLOAD_MICROREACT' {
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122 errorStrategy = 'ignore'
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123 }
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124 }
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125 }
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126
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127 // Method to instantiate a new function parser
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128 // Need to refactor using ScriptParser... another day
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129 def loadThisFunction (func_file) {
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130 GroovyShell grvy_sh = new GroovyShell()
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131 def func = grvy_sh.parse(new File ( func_file ) )
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132 return func
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133 }
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134
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135 // Method to add relevant final parameters to summary log
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136 def addParamsToSummary(Map params_to_add = [:]) {
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137
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138 if (!params_to_add.isEmpty()) {
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139 def not_null_params_to_add = params_to_add.findAll {
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140 it.value.clivalue != null &&
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141 it.value.clivalue != '[:]' &&
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142 it.value.clivalue != ''
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143 }
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144
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145 params.logtheseparams += not_null_params_to_add.keySet().toList()
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146
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147 return not_null_params_to_add.collect {
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148 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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149 }.join(' ').trim()
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150 }
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151 return 1
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152 } |
