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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 ${params.fq_filter_by_len}" : ''
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5 ].join(' ').trim()
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6 }
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7
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8 if (params.bbmerge_run) {
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9 withName: 'BBTOOLS_BBMERGE' {
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10 ext.args = addParamsToSummary(
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11 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
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12 )
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13 }
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14 }
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15
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16 if (params.fastp_run) {
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17 withName: 'FASTP' {
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18 ext.args = addParamsToSummary(
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19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
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20 )
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21 }
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22 }
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23
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24 if (params.bcs_concat_pe) {
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25 withName: 'CAT_CAT' {
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26 ext.prefix = 'concat.fastq.gz'
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27 }
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28 }
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29
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30
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31 if (params.mashscreen_run) {
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32 withName: 'MASH_SCREEN' {
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33 ext.args = addParamsToSummary(
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34 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
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35 )
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36 }
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37 }
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38
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39 if (params.tuspy_run) {
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40 withName: 'TOP_UNIQUE_SEROVARS' {
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41 ext.args = addParamsToSummary(
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42 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
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43 )
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44 }
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45 }
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46
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47 if (params.gsrpy_run) {
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48 withName: 'BCS_RESULTS' {
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49 ext.args = addParamsToSummary(
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50 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
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51 )
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52 }
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53 }
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54
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55 if (params.sourmashsketch_run) {
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56 withName: 'SOURMASH_SKETCH' {
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57 ext.args = addParamsToSummary(
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58 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
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59 )
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60 }
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61 }
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62
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63 if (params.sourmashgather_run) {
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64 withName: 'SOURMASH_GATHER' {
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65 ext.args = addParamsToSummary(
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66 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
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67 )
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68
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69 if (params.sfhpy_run) {
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70 ext.args2 = addParamsToSummary(
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71 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
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72 )
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73 }
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74 }
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75 }
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76
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77 if (params.sourmashsearch_run) {
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78 withName: 'SOURMASH_SEARCH' {
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79 ext.args = addParamsToSummary(
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80 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
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81 )
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82
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83 if (params.sfhpy_run) {
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84 ext.args2 = addParamsToSummary(
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85 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
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86 )
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87 }
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88 }
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89 }
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90
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91 if (params.kmaindex_run) {
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92 withName: 'KMA_INDEX' {
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93 ext.args = addParamsToSummary(
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94 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
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95 )
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96 }
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97 }
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98
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99 if (params.kmaalign_run) {
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100 withName: 'KMA_ALIGN' {
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101 ext.args = addParamsToSummary(
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102 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
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103 )
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104 }
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105 }
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106
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107 if (params.megahit_run) {
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108 withName: 'MEGAHIT_ASSEMBLE' {
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109 errorStrategy = 'ignore'
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110 ext.args = addParamsToSummary(
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111 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
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112 )
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113 }
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114
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115 withName: 'MLST' {
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116 ext.when = params.mlst_run
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117 ext.args = addParamsToSummary(
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118 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
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119 )
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120 }
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121
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122 withName: 'ABRICATE_RUN' {
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123 ext.when = params.abricate_run
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124 ext.args = addParamsToSummary(
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125 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
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126 )
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127 }
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128
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129 withName: 'ABRICATE_SUMMARY' {
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130 ext.when = params.abricate_summary_run
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131 }
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132 }
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133
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134 if (params.salmonidx_run) {
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135 withName: 'SALMON_INDEX' {
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136 ext.args = addParamsToSummary(
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137 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
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138 )
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139 }
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140 }
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141
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142 withName: 'OTF_GENOME' {
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143 errorStrategy = 'ignore'
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144 }
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145
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146 }
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147
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148
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149 // Parse the default params
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150 def loadThisFunction (func_file) {
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151 GroovyShell grvy_sh = new GroovyShell()
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152 def func = grvy_sh.parse(new File ( func_file ) )
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153 return func
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154 }
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155
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156 // Method to add relevant final parameters to summary log
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157 def addParamsToSummary(Map params_to_add = [:]) {
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158
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159 if (!params_to_add.isEmpty()) {
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160 def not_null_params_to_add = params_to_add.findAll {
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161 it.value.clivalue != null &&
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162 it.value.clivalue != '[:]' &&
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163 it.value.clivalue != ''
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164 }
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165
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166 params.logtheseparams += not_null_params_to_add.keySet().toList()
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167
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168 return not_null_params_to_add.collect {
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169 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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170 }.join(' ').trim()
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171 }
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172 return 1
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173 }
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