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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 "${params.routines}"
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9 include { dpubmlstpyHelp } from "${params.toolshelp}${params.fs}dpubmlstpy"
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10 include { checkm2predictHelp } from "${params.toolshelp}${params.fs}checkm2predict"
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11 include { guncrunHelp } from "${params.toolshelp}${params.fs}guncrun"
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12 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
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13
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14 // Exit if help requested before any subworkflows
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15 if (params.help) {
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16 log.info help()
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17 exit 0
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18 }
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19
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20 // Include any necessary modules and subworkflows
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21 include { DOWNLOAD_PDG_METADATA } from "${params.modules}${params.fs}download_pdg_metadata${params.fs}main"
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22 include { DOWNLOAD_PUBMLST_SCHEME } from "${params.modules}${params.fs}download_pubmlst_scheme${params.fs}main"
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23 include { FILTER_PDG_METADATA } from "${params.modules}${params.fs}filter_pdg_metadata${params.fs}main"
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24 include { GUNC_RUN } from "${params.modules}${params.fs}gunc${params.fs}run${params.fs}main"
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25 include { CHECKM2_PREDICT } from "${params.modules}${params.fs}checkm2${params.fs}predict${params.fs}main"
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26 include { QUAL_PASSED_GENOMES } from "${params.modules}${params.fs}custom${params.fs}qual_passed_genomes${params.fs}main"
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27 include { SCAFFOLD_GENOMES } from "${params.modules}${params.fs}scaffold_genomes${params.fs}main"
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28 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
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29 include { INDEX_PDG_METADATA } from "${params.modules}${params.fs}index_pdg_metadata${params.fs}main"
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30 include { MASH_SKETCH } from "${params.modules}${params.fs}mash${params.fs}sketch${params.fs}main"
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31 include { MASH_PASTE } from "${params.modules}${params.fs}mash${params.fs}paste${params.fs}main"
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32 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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33
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34 /*
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35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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36 INPUTS AND ANY CHECKS FOR THE CRONOLOGY_DB WORKFLOW
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37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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38 */
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39
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40 if (!params.output) {
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41 stopNow("Please mention the absolute UNIX path to store the DB flat files\n" +
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42 "using the --output option.\n" +
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43 "Ex: --output /path/to/cronology/db_files")
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44 }
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45
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46 checkDBPathExists(params.guncrun_dbpath, 'GUNC')
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47 checkDBPathExists(params.checkm2predict_dbpath, 'CheckM2')
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48
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49 /*
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50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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51 RUN THE CRONOLOGY_DB WORKFLOW
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52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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53 */
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54
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55 workflow CRONOLOGY_DB {
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56 main:
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57 log.info summaryOfParams()
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58
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59 DOWNLOAD_PDG_METADATA ( params.pdg_release ?: null )
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60
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61 DOWNLOAD_PDG_METADATA.out.versions
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62 .set { software_versions }
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63
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64 DOWNLOAD_PUBMLST_SCHEME ( params.dpubmlstpy_org ?: null )
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65
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66 FILTER_PDG_METADATA (
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67 DOWNLOAD_PDG_METADATA.out.accs
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68 .splitText(by: params.genomes_chunk, file: true)
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69 )
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70
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71 FILTER_PDG_METADATA.out.accs_chunk_tbl
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72 .collectFile(sort: { acc_f -> acc_f.simpleName })
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73 .multiMap { acc_chunk_file ->
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74 def meta = [:]
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75 meta.id = 'AssemblyQC'
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76 meta.phone_ncbi = true
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77 gunc: [ meta, params.guncrun_dbpath, acc_chunk_file ]
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78 checkm2: [ meta, params.checkm2predict_dbpath, acc_chunk_file ]
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79 }
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80 .set { ch_run_qual_on_these_accs }
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81
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82 CHECKM2_PREDICT ( ch_run_qual_on_these_accs.checkm2 )
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83
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84 GUNC_RUN ( ch_run_qual_on_these_accs.gunc )
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85
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86 QUAL_PASSED_GENOMES (
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87 CHECKM2_PREDICT.out.quality_report_passed
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88 .map { meta, qual ->
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89 [ qual ]
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90 }
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91 .collect()
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92 .flatten()
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93 .collectFile(name: 'checkm2_quality_passed.txt'),
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94 GUNC_RUN.out.quality_report_passed
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95 .map { meta, qual ->
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96 [ qual ]
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97 }
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98 .collect()
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99 .flatten()
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100 .collectFile(name: 'gunc_quality_passed.txt')
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101 )
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102
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103 SCAFFOLD_GENOMES (
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104 QUAL_PASSED_GENOMES.out.accs
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105 .splitText(by: params.genomes_chunk, file: true)
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106 )
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107
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108 SCAFFOLD_GENOMES.out.scaffolded
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109 .multiMap { scaffolded ->
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110 def meta = [:]
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111 meta.id = (params.pdg_release ?: 'NCBI Pathogen Genomes')
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112 mlst: [ meta, scaffolded ]
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113 mash: [ meta, scaffolded ]
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114 }
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115 .set { ch_scaffolded_genomes }
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116
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117 MLST (
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118 ch_scaffolded_genomes.mlst
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119 .combine( DOWNLOAD_PUBMLST_SCHEME.out.pubmlst_dir )
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120 )
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121
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122 MLST.out.tsv
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123 .map { meta, tsv ->
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124 tsv
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125 }
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126 .collectFile(
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127 name: 'mlst_results.tsv',
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128 keepHeader: true,
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129 skip: 1
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130 )
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131 .set { ch_mlst_results }
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132
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133 INDEX_PDG_METADATA (
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134 DOWNLOAD_PDG_METADATA.out.pdg_metadata,
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135 DOWNLOAD_PDG_METADATA.out.snp_cluster_metadata,
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136 DOWNLOAD_PDG_METADATA.out.accs,
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137 ch_mlst_results
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138 )
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139
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140 MASH_SKETCH (
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141 ch_scaffolded_genomes.mash
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142 .map { it -> tuple ( it[0], it[1].flatten() ) }
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143 )
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144
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145 MASH_PASTE (
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146 MASH_SKETCH.out.sketch
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147 .map { meta, sketch ->
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148 [ [id: (params.pdg_release ?: 'NCBI Pathogen Genomes')], sketch ]
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149 }
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150 .groupTuple(by: [0])
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151 )
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152
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153 DUMP_SOFTWARE_VERSIONS (
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154 software_versions
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155 .mix (
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156 DOWNLOAD_PDG_METADATA.out.versions,
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157 DOWNLOAD_PUBMLST_SCHEME.out.versions,
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158 FILTER_PDG_METADATA.out.versions,
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159 CHECKM2_PREDICT.out.versions,
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160 GUNC_RUN.out.versions,
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161 QUAL_PASSED_GENOMES.out.versions,
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162 SCAFFOLD_GENOMES.out.versions,
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163 MLST.out.versions,
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164 INDEX_PDG_METADATA.out.versions,
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165 MASH_SKETCH.out.versions,
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166 MASH_PASTE.out.versions
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167 )
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168 .unique()
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169 .collectFile(name: 'collected_versions.yml')
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170 )
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171 }
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172
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173 /*
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174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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175 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
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176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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177 */
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178
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179 workflow.onComplete {
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180 if (workflow.success) {
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181 sendMail()
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182 }
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183 }
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184
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185 workflow.onError {
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186 sendMail()
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187 }
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188
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189 /*
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190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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191 METHOD TO CHECK IF DB PATHS EXIST
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192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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193 */
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194
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195 def checkDBPathExists(db_path, msg) {
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196 db_path_obj = file( db_path )
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197
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198 if (!db_path_obj.exists()) {
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199 stopNow("Please check if the database path for ${msg}\n" +
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200 "[ ${db_path} ]\nexists.")
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201 }
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202 }/*
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203
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204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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205 HELP TEXT METHODS FOR CRONOLOGY WORKFLOW
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206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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207 */
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208
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209 def help() {
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210
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211 Map helptext = [:]
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212
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213 helptext.putAll (
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214 fastqEntryPointHelp().findAll {
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215 it.key =~ /Required|output|Other|Workflow|Author|Version/
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216 } +
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217 dpubmlstpyHelp(params).text +
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218 checkm2predictHelp(params).text +
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219 guncrunHelp(params).text +
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220 wrapUpHelp()
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221 )
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222
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223 return addPadding(helptext)
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224 } |
