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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 ${params.fq_filter_by_len}" : ''
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5 ].join(' ').trim()
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6 }
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7
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8 if (params.filtlong_run) {
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9 withName: 'FILTLONG' {
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10 ext.args = addParamsToSummary(
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11 loadThisFunction("${params.toolshelp}${params.fs}filtlong.nf").filtlongHelp(params).helpparams
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12 )
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13 }
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14 }
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15
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16 if (params.mashscreen_run) {
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17 withName: 'MASH_SCREEN' {
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18 ext.args = addParamsToSummary(
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19 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
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20 )
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21 }
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22 }
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23
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24 if (params.tuspy_run) {
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25 withName: 'TOP_UNIQUE_SEROVARS' {
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26 ext.args = addParamsToSummary(
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27 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
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28 )
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29 }
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30 }
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31
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32 if (params.gsrpy_run) {
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33 withName: 'BCS_RESULTS' {
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34 ext.args = addParamsToSummary(
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35 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
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36 )
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37 }
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38 }
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39
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40 if (params.sourmashsketch_run) {
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41 withName: 'SOURMASH_SKETCH' {
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42 ext.args = addParamsToSummary(
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43 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
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44 )
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45 }
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46 }
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47
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48 if (params.sourmashgather_run) {
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49 withName: 'SOURMASH_GATHER' {
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50 ext.args = addParamsToSummary(
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51 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
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52 )
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53
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54 if (params.sfhpy_run) {
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55 ext.args2 = addParamsToSummary(
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56 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
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57 )
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58 }
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59 }
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60 }
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61
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62 if (params.sourmashsearch_run) {
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63 withName: 'SOURMASH_SEARCH' {
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64 ext.args = addParamsToSummary(
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65 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
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66 )
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67
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68 if (params.sfhpy_run) {
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69 ext.args2 = addParamsToSummary(
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70 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
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71 )
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72 }
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73 }
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74 }
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75
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76 if (params.flye_run) {
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77 withName: 'FLYE_ASSEMBLE' {
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78 errorStrategy = 'ignore'
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79 ext.args = addParamsToSummary(
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80 loadThisFunction("${params.toolshelp}${params.fs}flye.nf").flyeHelp(params).helpparams
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81 )
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82 }
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83
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84 withName: 'MINIMAP2_ALIGN' {
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85 ext.args = '-ax map-ont'
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86 }
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87
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88 withName: 'MLST' {
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89 ext.when = params.mlst_run
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90 ext.args = addParamsToSummary(
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91 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
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92 )
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93 }
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94
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95 withName: 'ABRICATE_RUN' {
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96 ext.when = params.abricate_run
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97 ext.args = addParamsToSummary(
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98 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
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99 )
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100 }
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101
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102 withName: 'ABRICATE_SUMMARY' {
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103 ext.when = params.abricate_summary_run
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104 }
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105 }
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106
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107 withName: 'SALMON_QUANT' {
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108 ext.args = '--ont'
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109 }
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110
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111 withName: 'OTF_GENOME' {
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112 errorStrategy = 'ignore'
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113 }
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114
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115 }
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116
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117
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118 // Parse the default params
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119 def loadThisFunction (func_file) {
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120 GroovyShell grvy_sh = new GroovyShell()
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121 def func = grvy_sh.parse(new File ( func_file ) )
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122 return func
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123 }
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124
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125 // Method to add relevant final parameters to summary log
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126 def addParamsToSummary(Map params_to_add = [:]) {
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127
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128 if (!params_to_add.isEmpty()) {
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129 def not_null_params_to_add = params_to_add.findAll {
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130 it.value.clivalue != null &&
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131 it.value.clivalue != '[:]' &&
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132 it.value.clivalue != ''
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133 }
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134
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135 params.logtheseparams += not_null_params_to_add.keySet().toList()
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136
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137 return not_null_params_to_add.collect {
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138 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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139 }.join(' ').trim()
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140 }
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141 return 1
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142 }
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