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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 ${params.fq_filter_by_len}" : ''
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5 ].join(' ').trim()
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6 }
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7
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8 // withName: 'SAMTOOLS_FASTQ' {
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9 // ext.args = (params.fq_single_end ? '-F 4' : '-f 2')
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10 // }
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11
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12 if (params.fastp_run) {
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13 withName: 'FASTP' {
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14 ext.args = addParamsToSummary(
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15 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
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16 )
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17 }
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18 }
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19
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20 if (params.kmaalign_run) {
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21 withName: 'KMA_ALIGN' {
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22 ext.args = addParamsToSummary(
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23 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
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24 )
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25 }
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26 }
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27
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28 if (params.seqkit_grep_run) {
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29 withName: 'SEQKIT_GREP' {
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30 ext.args = addParamsToSummary(
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31 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
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32 )
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33 }
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34 }
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35
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36 if (params.salmonidx_run){
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37 withName: 'SALMON_INDEX' {
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38 ext.args = addParamsToSummary(
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39 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
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40 )
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41 }
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42
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43 withName: 'SALMON_QUANT' {
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44 errorStrategy = 'ignore'
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45 ext.args = '--minAssignedFrags 1'
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46 }
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47 }
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48
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49 if (params.sourmashsketch_run) {
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50 withName: 'SOURMASH_SKETCH' {
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51 ext.args = addParamsToSummary(
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52 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
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53 )
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54 }
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55 }
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56
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57 if (params.sourmashgather_run) {
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58 withName: 'SOURMASH_GATHER' {
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59 ext.args = addParamsToSummary(
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60 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
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61 )
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62
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63 if (params.sfhpy_run) {
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64 ext.args2 = addParamsToSummary(
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65 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
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66 )
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67 }
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68 }
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69 }
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70
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71 // if (params.sourmashtaxmetagenome_run) {
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72 // withName: 'SOURMASH_TAX_METAGENOME' {
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73 // ext.args = addParamsToSummary(
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74 // loadThisFunction("${params.toolshelp}${params.fs}sourmashtaxmetagenome.nf").sourmashtaxmetagenomeHelp(params).helpparams
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75 // )
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76 // }
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77 // }
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78
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79 if (params.gsalkronapy_run) {
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80 withName: 'NOWAYOUT_RESULTS' {
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81 ext.args = addParamsToSummary(
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82 loadThisFunction("${params.toolshelp}${params.fs}gsalkronapy.nf").gsalkronapyHelp(params).helpparams
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83 )
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84 }
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85 }
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86
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87 if (params.krona_ktIT_run) {
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88 withName: 'KRONA_KTIMPORTTEXT' {
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89 ext.args = addParamsToSummary(
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90 loadThisFunction("${params.toolshelp}${params.fs}kronaktimporttext.nf").kronaktimporttextHelp(params).helpparams
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91 )
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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 // Method to instantiate a new function parser
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97 // Need to refactor using ScriptParser... another day
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98 def loadThisFunction (func_file) {
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99 GroovyShell grvy_sh = new GroovyShell()
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100 def func = grvy_sh.parse(new File ( func_file ) )
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101 return func
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102 }
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103
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104 // Method to add relevant final parameters to summary log
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105 def addParamsToSummary(Map params_to_add = [:]) {
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106
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107 if (!params_to_add.isEmpty()) {
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108 def not_null_params_to_add = params_to_add.findAll {
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109 it.value.clivalue != null &&
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110 it.value.clivalue != '[:]' &&
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111 it.value.clivalue != ''
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112 }
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113
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114 params.logtheseparams += not_null_params_to_add.keySet().toList()
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115
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116 return not_null_params_to_add.collect {
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117 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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118 }.join(' ').trim()
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119 }
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120 return 1
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121 } |
