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1 // Define any required imports for this specific workflow
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2 import java.nio.file.Paths
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3 import nextflow.file.FileHelper
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4
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5 // Include any necessary methods
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6 include { \
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7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
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8 addPadding; wrapUpHelp } from "${params.routines}"
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9 include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2"
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10 include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge"
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11 include { spadesHelp } from "${params.toolshelp}${params.fs}spades"
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12 include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder"
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13 include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2"
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14 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
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15 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
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16
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17 // Exit if help requested before any subworkflows
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18 if (params.help) {
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19 log.info help()
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20 exit 0
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21 }
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22
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23 // Include any necessary modules and subworkflows
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24 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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25 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
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26 include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main"
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27 include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main"
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28 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
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29 include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main"
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30 include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main"
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31 include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main"
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32 include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main"
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33 include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main"
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34 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
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35 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
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36 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
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37 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
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38 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
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39 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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45 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN-HY WORKFLOW
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46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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47 */
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48
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49 def kraken2_db_dir = file ( "${params.kraken2_db}" )
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50 def centrifuge_x = file ( "${params.centrifuge_x}" )
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51 def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false)
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52 def reads_platform = 0
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53 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
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54
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55 reads_platform += (params.input ? 1 : 0)
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56
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57 if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) {
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58 stopNow("Please check if the following absolute paths are valid:\n" +
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59 "${params.kraken2_db}\n${params.centrifuge_x}\n" +
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60 "Cannot proceed further!")
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61 }
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62
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63 if (spades_custom_hmm && !spades_custom_hmm.exists()) {
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64 stopNow("Please check if the following SPAdes' custom HMM directory\n" +
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65 "path is valid:\n${params.spades_hmm}\nCannot proceed further!")
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66 }
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67
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68 if (reads_platform < 1 || reads_platform == 0) {
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69 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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70 "FASTQ files sequenced using the --input option.\n" +
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71 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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72 }
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73
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74 if (params.centrifuge_extract_bug != params.kraken2_extract_bug) {
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75 stopNow("Please make sure that the bug to be extracted is same\n" +
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76 "for both --centrifuge_extract_bug and --kraken2_extract_bug options.")
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77 }
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78
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79 /*
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80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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81 RUN THE CENTRIFLAKEN-HY WORKFLOW
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82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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83 */
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84
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85 workflow CENTRIFLAKEN_HY {
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86 main:
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87 ch_asm_filtered_contigs = Channel.empty()
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88 ch_mqc_custom_tbl = Channel.empty()
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89 ch_dummy = Channel.fromPath("${params.dummyfile}")
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90 ch_dummy2 = Channel.fromPath("${params.dummyfile2}")
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91
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92 log.info summaryOfParams()
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93
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94 PROCESS_FASTQ()
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95 .processed_reads
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96 .map {
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97 meta, fastq ->
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98 meta.centrifuge_x = params.centrifuge_x
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99 meta.kraken2_db = params.kraken2_db
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100 [meta, fastq]
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101 }
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102 .set { ch_processed_reads }
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103
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104 PROCESS_FASTQ
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105 .out
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106 .versions
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107 .set { software_versions }
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108
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109 FASTQC ( ch_processed_reads )
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110
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111 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
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112
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113 CENTRIFUGE_PROCESS (
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114 CENTRIFUGE_CLASSIFY.out.report
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115 .join( CENTRIFUGE_CLASSIFY.out.output )
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116 )
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117
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118 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
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119 .set { ch_centrifuge_extracted }
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120
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121 SEQKIT_GREP ( ch_centrifuge_extracted )
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122
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123 // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do
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kkonganti@0
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124 // allowNull: true for both input and output, but until then, we have to use dummy files.
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125 // and work arounds.
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126 // https://github.com/nextflow-io/nextflow/pull/2893
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127 SPADES_ASSEMBLE (
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128 SEQKIT_GREP.out.fastx
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129 .combine(ch_dummy)
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130 .combine(ch_dummy2)
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131 )
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132
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133 SPADES_ASSEMBLE
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134 .out
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135 .assembly
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136 .set { ch_spades_assembly }
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137
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138 ch_spades_assembly
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139 .map {
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140 meta, fastq ->
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141 meta.is_assembly = true
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142 [meta, fastq]
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143 }
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144 .set { ch_spades_assembly }
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145
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146 ch_spades_assembly.ifEmpty { [ false, false ] }
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147
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148 KRAKEN2_CLASSIFY ( ch_spades_assembly )
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149
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150 KRAKEN2_EXTRACT_CONTIGS (
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151 ch_spades_assembly
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152 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
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153 params.kraken2_extract_bug
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154 )
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155
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156 KRAKEN2_EXTRACT_CONTIGS
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157 .out
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158 .asm_filtered_contigs
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159 .map {
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160 meta, fastq ->
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161 meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize()
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162 meta.serotypefinder_db = params.serotypefinder_db
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163 [meta, fastq]
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164 }
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165 .set { ch_asm_filtered_contigs }
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166
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167 SEROTYPEFINDER ( ch_asm_filtered_contigs )
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168
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169 SEQSERO2 ( ch_asm_filtered_contigs )
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170
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171 MLST ( ch_asm_filtered_contigs )
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172
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173 ABRICATE_RUN (
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174 ch_asm_filtered_contigs,
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175 abricate_dbs
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176 )
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177
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kkonganti@0
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178 ABRICATE_RUN
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179 .out
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180 .abricated
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kkonganti@0
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181 .map { meta, abres -> [ abricate_dbs, abres ] }
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182 .groupTuple(by: [0])
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kkonganti@0
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183 .map { it -> tuple ( it[0], it[1].flatten() ) }
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184 .set { ch_abricated }
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185
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186 ABRICATE_SUMMARY ( ch_abricated )
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187
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188 CENTRIFUGE_CLASSIFY.out.kreport
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189 .map { meta, kreport -> [ kreport ] }
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190 .flatten()
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191 .concat (
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192 KRAKEN2_CLASSIFY.out.kraken_report
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kkonganti@0
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193 .map { meta, kreport -> [ kreport ] }
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kkonganti@0
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194 .flatten(),
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195 FASTQC.out.zip
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196 .map { meta, zip -> [ zip ] }
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197 .flatten()
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198 )
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199 .set { ch_mqc_classify }
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200
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201 if (params.serotypefinder_run) {
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202 SEROTYPEFINDER
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203 .out
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kkonganti@0
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204 .serotyped
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kkonganti@0
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205 .map { meta, tsv -> [ 'serotypefinder', tsv ] }
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kkonganti@0
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206 .groupTuple(by: [0])
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kkonganti@0
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207 .map { it -> tuple ( it[0], it[1].flatten() ) }
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kkonganti@0
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208 .set { ch_mqc_custom_tbl }
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kkonganti@0
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209 } else if (params.seqsero2_run) {
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210 SEQSERO2
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211 .out
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kkonganti@0
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212 .serotyped
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kkonganti@0
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213 .map { meta, tsv -> [ 'seqsero2', tsv ] }
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214 .groupTuple(by: [0])
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kkonganti@0
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215 .map { it -> tuple ( it[0], it[1].flatten() ) }
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216 .set { ch_mqc_custom_tbl }
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217 }
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218
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219 ch_mqc_custom_tbl
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220 .concat (
|
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221 ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )},
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222 ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )},
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kkonganti@0
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223 ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )},
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kkonganti@0
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224 ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )},
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225 )
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226 .groupTuple(by: [0])
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kkonganti@0
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227 .map { it -> [ it[0], it[1].flatten() ]}
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228 .set { ch_mqc_custom_tbl }
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229
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230 TABLE_SUMMARY ( ch_mqc_custom_tbl )
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231
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232 DUMP_SOFTWARE_VERSIONS (
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233 software_versions
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kkonganti@0
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234 .mix (
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235 FASTQC.out.versions,
|
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236 CENTRIFUGE_CLASSIFY.out.versions,
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237 CENTRIFUGE_PROCESS.out.versions,
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238 SEQKIT_GREP.out.versions,
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239 SPADES_ASSEMBLE.out.versions.ifEmpty(null),
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240 KRAKEN2_CLASSIFY.out.versions.ifEmpty(null),
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241 KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null),
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kkonganti@0
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242 SEROTYPEFINDER.out.versions.ifEmpty(null),
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243 SEQSERO2.out.versions.ifEmpty(null),
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244 MLST.out.versions.ifEmpty(null),
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kkonganti@0
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245 ABRICATE_RUN.out.versions.ifEmpty(null),
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kkonganti@0
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246 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
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247 TABLE_SUMMARY.out.versions.ifEmpty(null)
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kkonganti@0
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248 )
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249 .unique()
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250 .collectFile(name: 'collected_versions.yml')
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251 )
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kkonganti@0
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252
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kkonganti@0
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253 DUMP_SOFTWARE_VERSIONS
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254 .out
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255 .mqc_yml
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kkonganti@0
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256 .concat (
|
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257 ch_mqc_classify,
|
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258 TABLE_SUMMARY.out.mqc_yml
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kkonganti@0
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259 )
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kkonganti@0
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260 .collect()
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kkonganti@0
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261 .set { ch_multiqc }
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kkonganti@0
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262
|
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263 MULTIQC ( ch_multiqc )
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kkonganti@0
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264 }
|
kkonganti@0
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265
|
kkonganti@0
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266 /*
|
kkonganti@0
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267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
kkonganti@0
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268 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
|
kkonganti@0
|
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
kkonganti@0
|
270 */
|
kkonganti@0
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271
|
kkonganti@0
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272 workflow.onComplete {
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kkonganti@0
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273 if (workflow.success) {
|
kkonganti@0
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274 // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S)
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kkonganti@0
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275 //
|
kkonganti@0
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276 // Nextflow's .moveTo will error out if directories contain files and it
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kkonganti@0
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277 // would be complex to include logic to skip directories
|
kkonganti@0
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278 //
|
kkonganti@0
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279 def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps"
|
kkonganti@0
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280 def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results"
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kkonganti@0
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281 def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' )
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kkonganti@0
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282 def final_intermediate = file( final_intermediate_dir, type: 'dir' )
|
kkonganti@0
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283 def final_results = file( final_results_dir, type: 'dir' )
|
kkonganti@0
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284 def pipeline_output = file( params.output, type: 'dir' )
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kkonganti@0
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285
|
kkonganti@0
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286 if ( !final_intermediate.exists() ) {
|
kkonganti@0
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287 final_intermediate.mkdirs()
|
kkonganti@0
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288
|
kkonganti@0
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289 FileHelper.visitFiles(Paths.get("${params.output}"), '*') {
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kkonganti@0
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290 if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) {
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kkonganti@0
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291 FileHelper.movePath(
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kkonganti@0
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292 it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" )
|
kkonganti@0
|
293 )
|
kkonganti@0
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294 }
|
kkonganti@0
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295 }
|
kkonganti@0
|
296 }
|
kkonganti@0
|
297
|
kkonganti@0
|
298 if ( kraken2_ext_contigs.exists() && !final_results.exists() ) {
|
kkonganti@0
|
299 final_results.mkdirs()
|
kkonganti@0
|
300
|
kkonganti@0
|
301 FileHelper.movePath(
|
kkonganti@0
|
302 Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ),
|
kkonganti@0
|
303 Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" )
|
kkonganti@0
|
304 )
|
kkonganti@0
|
305 }
|
kkonganti@0
|
306
|
kkonganti@0
|
307 sendMail()
|
kkonganti@0
|
308 }
|
kkonganti@0
|
309 }
|
kkonganti@0
|
310
|
kkonganti@0
|
311 workflow.onError {
|
kkonganti@0
|
312 sendMail()
|
kkonganti@0
|
313 }
|
kkonganti@0
|
314
|
kkonganti@0
|
315 /*
|
kkonganti@0
|
316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
kkonganti@0
|
317 HELPER METHODS FOR CENTRIFLAKEN-HY WORKFLOW
|
kkonganti@0
|
318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
kkonganti@0
|
319 */
|
kkonganti@0
|
320
|
kkonganti@0
|
321 def help() {
|
kkonganti@0
|
322
|
kkonganti@0
|
323 Map helptext = [:]
|
kkonganti@0
|
324
|
kkonganti@47
|
325 helptext.putAll (
|
kkonganti@0
|
326 fastqEntryPointHelp() +
|
kkonganti@0
|
327 kraken2Help(params).text +
|
kkonganti@0
|
328 centrifugeHelp(params).text +
|
kkonganti@0
|
329 spadesHelp(params).text +
|
kkonganti@0
|
330 serotypefinderHelp(params).text +
|
kkonganti@0
|
331 seqsero2Help(params).text +
|
kkonganti@0
|
332 mlstHelp(params).text +
|
kkonganti@0
|
333 abricateHelp(params).text +
|
kkonganti@0
|
334 wrapUpHelp()
|
kkonganti@0
|
335 )
|
kkonganti@0
|
336
|
kkonganti@0
|
337 return addPadding(helptext)
|
kkonganti@0
|
338 } |