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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 ${params.fq_filter_by_len}" : ''
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5 ].join(' ').trim()
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6 }
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7
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8 if (params.seqkit_rmdup_run) {
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9 withName: 'SEQKIT_RMDUP' {
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10 ext.when = params.seqkit_rmdup_run
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11 ext.args = addParamsToSummary(
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12 loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
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13 )
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14 }
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15 }
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16
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17 if (params.seqkit_grep_on) {
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18 withName: 'SEQKIT_GREP' {
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19 ext.args = addParamsToSummary(
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20 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
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21 )
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22 }
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23 }
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24
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25 withName: 'CENTRIFUGE_CLASSIFY' {
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26 ext.args = addParamsToSummary(
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27 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
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28 )
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29 }
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30
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31 withName: 'KRAKEN2_CLASSIFY' {
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32 ext.args = addParamsToSummary(
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33 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
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34 )
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35 }
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36
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37 withName: 'MEGAHIT_ASSEMBLE' {
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38 ext.when = params.megahit_run
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39 errorStrategy = 'ignore'
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40 ext.args = addParamsToSummary(
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41 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
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42 )
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43 }
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44
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45 withName: 'SPADES_ASSEMBLE' {
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46 ext.when = params.spades_run
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47 errorStrategy = 'ignore'
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48 ext.args = addParamsToSummary(
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49 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
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50 )
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51 }
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52
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53 if (params.ectyper_run) {
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54 withName: 'ECTYPER' {
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55 ext.when = params.ectyper_run
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56 ext.args = addParamsToSummary(
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57 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
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58 )
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59 }
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60 }
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61
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62 withName: 'SEROTYPEFINDER' {
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63 ext.when = params.serotypefinder_run
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64 ext.args = addParamsToSummary(
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65 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
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66 )
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67 }
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68
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69 withName: 'SEQSERO2' {
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70 ext.when = params.seqsero2_run
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71 ext.args = addParamsToSummary(
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72 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
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73 )
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74 }
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75
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76 withName: 'MLST' {
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77 ext.when = params.mlst_run
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78 ext.args = addParamsToSummary(
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79 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
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80 )
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81 }
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82
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83 if (params.amrfinderplus_run) {
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84 withName: 'AMRFINDERPLUS_RUN' {
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85 ext.when = params.amrfinderplus_run
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86 ext.args = addParamsToSummary(
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87 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
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88 )
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89 }
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90 }
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91
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92 withName: 'ABRICATE_RUN' {
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93 ext.when = params.abricate_run
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94 ext.args = addParamsToSummary(
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95 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
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96 )
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97 }
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98
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99 withName: 'ABRICATE_SUMMARY' {
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100 ext.when = params.abricate_summary_run
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101 }
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102 }
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103
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104 // Method to instantiate a new function parser
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105 // Need to refactor using ScriptParser... another day
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106 def loadThisFunction (func_file) {
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107 GroovyShell grvy_sh = new GroovyShell()
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108 def func = grvy_sh.parse(new File ( func_file ) )
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109 return func
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110 }
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111
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112 // Method to add relevant final parameters to summary log
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113 def addParamsToSummary(Map params_to_add = [:]) {
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114
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115 if (!params_to_add.isEmpty()) {
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116 def not_null_params_to_add = params_to_add.findAll {
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117 it.value.clivalue != null &&
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118 it.value.clivalue != '[:]' &&
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119 it.value.clivalue != ''
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120 }
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121
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122 params.logtheseparams += not_null_params_to_add.keySet().toList()
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123
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124 return not_null_params_to_add.collect {
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125 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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126 }.join(' ').trim()
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127 }
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128 return 1
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129 } |
