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