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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; conciseHelp; \
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8 addPadding; wrapUpHelp } from "${params.routines}"
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9 include { dpubmlstpyHelp } from "${params.toolshelp}${params.fs}dpubmlstpy"
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10 include { fastpHelp } from "${params.toolshelp}${params.fs}fastp"
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11 include { mashscreenHelp } from "${params.toolshelp}${params.fs}mashscreen"
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12 include { tuspyHelp } from "${params.toolshelp}${params.fs}tuspy"
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13 include { spadesHelp } from "${params.toolshelp}${params.fs}spades"
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14 include { shovillHelp } from "${params.toolshelp}${params.fs}shovill"
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15 include { polypolishHelp } from "${params.toolshelp}${params.fs}polypolish"
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16 include { mashtreeHelp } from "${params.toolshelp}${params.fs}mashtree"
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17 include { quastHelp } from "${params.toolshelp}${params.fs}quast"
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18 include { prodigalHelp } from "${params.toolshelp}${params.fs}prodigal"
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19 include { prokkaHelp } from "${params.toolshelp}${params.fs}prokka"
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20 include { pirateHelp } from "${params.toolshelp}${params.fs}pirate"
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21 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
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22 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
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23
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24 // Exit if help requested before any subworkflows
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25 if (params.help) {
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26 log.info help()
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27 exit 0
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28 }
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29
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30 // Include any necessary modules and subworkflows
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31 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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32 include { PRODKA } from "${params.subworkflows}${params.fs}prodka"
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33 include { DOWNLOAD_PUBMLST_SCHEME } from "${params.modules}${params.fs}download_pubmlst_scheme${params.fs}main"
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34 include { DOWNLOAD_REF_GENOME } from "${params.modules}${params.fs}download_ref_genome${params.fs}main"
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35 include { FASTP } from "${params.modules}${params.fs}fastp${params.fs}main"
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36 include { MASH_SCREEN } from "${params.modules}${params.fs}mash${params.fs}screen${params.fs}main"
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37 include { TOP_UNIQUE_SEROVARS } from "${params.modules}${params.fs}top_unique_serovars${params.fs}main"
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38 include { CAT_UNIQUE } from "${params.modules}${params.fs}cat${params.fs}unique${params.fs}main"
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39 include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main"
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40 include { SHOVILL } from "${params.modules}${params.fs}shovill${params.fs}main"
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41 include { BWA_IDX_MEM } from "${params.modules}${params.fs}custom${params.fs}bwa_idx_mem${params.fs}main"
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42 include { POLYPOLISH } from "${params.modules}${params.fs}polypolish${params.fs}main"
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43 include { QUAST } from "${params.modules}${params.fs}quast${params.fs}main"
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44 include { RMLST_POST } from "${params.modules}${params.fs}rmlst${params.fs}main"
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45 include { PIRATE } from "${params.modules}${params.fs}pirate${params.fs}main"
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46 include { MASHTREE } from "${params.modules}${params.fs}mashtree${params.fs}main"
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47 include { UPLOAD_MICROREACT } from "${params.modules}${params.fs}upload_microreact${params.fs}main"
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48 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
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49 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
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50 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
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51 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
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52 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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53 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
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54
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55 /*
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56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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57 INPUTS AND ANY CHECKS FOR THE CRONOLOGY WORKFLOW
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58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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59 */
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60 def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false)
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61 def reads_platform = 0
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62 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
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63
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64 reads_platform += (params.input ? 1 : 0)
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65
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66 if (params.upload_microreact) {
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67 checkMetadataExists(params.microreact_api_key, 'Microreact API Key')
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68 }
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69
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70 if (spades_custom_hmm && !spades_custom_hmm.exists()) {
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71 stopNow("Please check if the following SPAdes' custom HMM directory\n" +
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72 "path is valid:\n${params.spades_hmm}\nCannot proceed further!")
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73 }
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74
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75 if (reads_platform < 1 || reads_platform == 0) {
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76 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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77 "FASTQ files sequenced using the --input option.\n" +
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78 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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79 }
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80
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81 /*
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82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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83 RUN THE CRONOLOGY WORKFLOW
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84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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85 */
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86
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87 workflow CRONOLOGY {
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88 main:
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89 ch_mqc_custom_tbl = Channel.empty()
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90 ch_dummy = Channel.fromPath("${params.dummyfile}")
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91 ch_dummy2 = Channel.fromPath("${params.dummyfile2}")
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92
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93 log.info summaryOfParams()
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94
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95 PROCESS_FASTQ()
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96
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97 PROCESS_FASTQ.out.versions
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98 .set { software_versions }
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99
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100 PROCESS_FASTQ.out.processed_reads
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101 .map { meta, fastq ->
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102 meta.sequence_sketch = (params.mash_sketch ?: null)
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103 [meta, fastq]
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104 }
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105 .set { ch_processed_reads }
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106
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107 DOWNLOAD_PUBMLST_SCHEME( params.dpubmlstpy_org ?: null )
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108
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109 DOWNLOAD_REF_GENOME(
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110 (params.ref_acc ? ['id': params.ref_acc] : null)
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111 )
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112
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113 FASTP( ch_processed_reads )
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114
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115 FASTP.out.passed_reads
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116 .set { ch_processed_reads }
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117
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118 FASTP.out.json
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119 .map { meta, json -> [ json ] }
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120 .collect()
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121 .set { ch_multiqc }
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122
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123 MASH_SCREEN( ch_processed_reads )
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124
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125 TOP_UNIQUE_SEROVARS( MASH_SCREEN.out.screened )
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126
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127 TOP_UNIQUE_SEROVARS.out.tsv
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128 .map { meta, tsv -> tsv }
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129 .collectFile(
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130 name: 'iTOL_metadata_w_dups.txt',
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131 keepHeader: true,
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132 skip: 4,
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133 sort: true
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134 )
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135 .map { file ->
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136 def meta = [:]
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137 meta.id = 'Unique iTOL Metadata'
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138 meta.skip_header = 4
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139 [meta, file]
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140 }
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141 .concat(
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142 TOP_UNIQUE_SEROVARS.out.popup
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143 .map { meta, popup -> popup }
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144 .collectFile(
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145 name: 'iTOL_2_NCBI_Pathogens_w_dups.txt',
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146 keepHeader: true,
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147 skip: 3,
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148 sort: true
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149 )
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150 .map { file ->
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151 def meta = [:]
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152 meta.id = 'Unique iTOL Popup'
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153 meta.skip_header = 3
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154 [meta, file]
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155 }
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156 )
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157 .set { ch_uniq }
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158
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159 TOP_UNIQUE_SEROVARS.out.accessions
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160 .map { meta, acc -> acc }
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161 .splitText()
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162 .collect()
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163 .flatten()
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164 .unique()
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165 .collectFile(name: 'tree_genomes.txt')
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166 .map { genomes -> [ [id: 'hitsTree'], genomes ]}
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167 .set { ch_genomes_fofn }
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168
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169 CAT_UNIQUE( ch_uniq )
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170
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171 if (params.fq_single_end) {
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172 SPADES_ASSEMBLE(
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173 ch_processed_reads
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174 .combine(ch_dummy)
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175 .combine(ch_dummy2)
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176 )
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177
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178 SPADES_ASSEMBLE.out.assembly
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179 .set{ ch_assembly }
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180
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181 software_versions
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182 .mix( SPADES_ASSEMBLE.out.versions.ifEmpty(null) )
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183 .set { software_versions }
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184 } else {
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185 SHOVILL( ch_processed_reads )
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186
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187 SHOVILL.out.contigs
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188 .set { ch_assembly }
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189
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190 software_versions
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191 .mix( SHOVILL.out.versions.ifEmpty(null) )
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192 .set { software_versions }
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193 }
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194
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195 if (params.polypolish_run) {
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196 BWA_IDX_MEM(
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197 ch_assembly
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198 .join( ch_processed_reads )
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199 )
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200
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201 POLYPOLISH(
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202 ch_assembly
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203 .join( BWA_IDX_MEM.out.aligned_sam )
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204 )
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205
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206 POLYPOLISH.out.polished
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207 .set { ch_assembly }
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208
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209 software_versions
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210 .mix(
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211 BWA_IDX_MEM.out.versions,
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212 POLYPOLISH.out.versions
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213 )
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214 .set { software_versions }
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215 }
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216
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217 ch_assembly
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218 .combine( DOWNLOAD_REF_GENOME.out.fasta )
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219 .combine( DOWNLOAD_REF_GENOME.out.gff )
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220 .multiMap { meta, consensus, fasta, gff ->
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221 sample_fa: consensus
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222 polished: [meta, consensus]
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223 ref_fasta: [meta, fasta]
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224 ref_gff: [meta, gff]
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225 }
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226 .set { ch_quast }
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227
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228 MASHTREE(
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229 ch_genomes_fofn,
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230 DOWNLOAD_REF_GENOME.out.fasta
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231 .concat( ch_quast.sample_fa )
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232 .collect()
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233 )
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234
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235 if (params.upload_microreact) {
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236 UPLOAD_MICROREACT(
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237 MASHTREE.out.nwk
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238 .map { meta, nwk ->
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239 nwk
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240 },
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241 CAT_UNIQUE.out.csv
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242 )
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243
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244 software_versions
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245 .mix(
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246 UPLOAD_MICROREACT.out.versions
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247 )
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248 .set { software_versions }
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249 }
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250
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251 PRODKA(
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252 ch_quast.ref_fasta,
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253 ch_quast.polished
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254 )
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255
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256 RMLST_POST( ch_assembly )
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257
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258 MLST (
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259 ch_assembly
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260 .combine( DOWNLOAD_PUBMLST_SCHEME.out.pubmlst_dir )
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261 )
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262
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263 QUAST(
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264 ch_quast.polished,
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265 ch_quast.ref_fasta,
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266 ch_quast.ref_gff
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267 )
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268
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269 if (params.pirate_run) {
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270 PIRATE(
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271 PRODKA.out.prokka_gff
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272 .map { meta, gff ->
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273 tuple( [id: 'Predicted Genes'], gff )
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274 }
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275 .groupTuple(by: [0])
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276 )
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277
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278 software_versions
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279 .mix( PIRATE.out.versions )
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280 .set { software_versions }
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281 }
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282
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283 RMLST_POST.out.tsv
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284 .map { meta, tsv -> [ 'rmlst', tsv] }
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285 .groupTuple(by: [0])
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286 .map { it -> tuple ( it[0], it[1].flatten() ) }
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287 .set { ch_mqc_rmlst_tbl }
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288
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289 MLST.out.tsv
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290 .map { meta, tsv -> [ 'mlst', tsv] }
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291 .groupTuple(by: [0])
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292 .map { it -> tuple ( it[0], it[1].flatten() ) }
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293 .set { ch_mqc_custom_tbl }
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294
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295 ABRICATE_RUN ( ch_assembly, abricate_dbs )
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296
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297 ABRICATE_RUN.out.abricated
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298 .map { meta, abres -> [ abricate_dbs, abres ] }
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299 .groupTuple(by: [0])
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300 .map { it -> tuple ( it[0], it[1].flatten() ) }
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301 .set { ch_abricated }
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302
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303 ABRICATE_SUMMARY ( ch_abricated )
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304
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305 ch_mqc_custom_tbl
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306 .concat (
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307 ch_mqc_rmlst_tbl,
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308 ABRICATE_SUMMARY.out.ncbiamrplus.map { it -> tuple ( it[0], it[1] )},
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309 ABRICATE_SUMMARY.out.resfinder.map { it -> tuple ( it[0], it[1] )},
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310 ABRICATE_SUMMARY.out.megares.map { it -> tuple ( it[0], it[1] )},
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311 ABRICATE_SUMMARY.out.argannot.map { it -> tuple ( it[0], it[1] )},
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312 )
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313 .groupTuple(by: [0])
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314 .map { it -> [ it[0], it[1].flatten() ]}
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315 .set { ch_mqc_custom_tbl }
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316
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317 TABLE_SUMMARY ( ch_mqc_custom_tbl )
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318
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319 DUMP_SOFTWARE_VERSIONS (
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320 software_versions
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321 .mix(
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322 DOWNLOAD_PUBMLST_SCHEME.out.versions,
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323 DOWNLOAD_REF_GENOME.out.versions,
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324 FASTP.out.versions,
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325 MASH_SCREEN.out.versions,
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326 TOP_UNIQUE_SEROVARS.out.versions,
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327 CAT_UNIQUE.out.versions,
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328 MASHTREE.out.versions,
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329 POLYPOLISH.out.versions,
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330 QUAST.out.versions,
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331 PRODKA.out.versions,
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332 RMLST_POST.out.versions,
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333 MLST.out.versions,
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334 ABRICATE_RUN.out.versions,
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335 ABRICATE_SUMMARY.out.versions,
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336 TABLE_SUMMARY.out.versions
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337 )
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338 .unique()
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339 .collectFile(name: 'collected_versions.yml')
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340 )
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341
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342 DUMP_SOFTWARE_VERSIONS.out.mqc_yml
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343 .concat (
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344 ch_multiqc,
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345 TABLE_SUMMARY.out.mqc_yml,
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346 PRODKA.out.prokka_txt.map { meta, txt -> txt },
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347 QUAST.out.results.map { meta, res -> res }
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348 )
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349 .collect()
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350 .set { ch_multiqc }
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351
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352 MULTIQC( ch_multiqc )
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353 }
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354
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355 /*
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356 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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357 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
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358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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359 */
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360
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361 workflow.onComplete {
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362 if (workflow.success) {
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363 sendMail()
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364 }
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365 }
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366
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367 workflow.onError {
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368 sendMail()
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369 }
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370
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371 /*
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372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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373 METHOD TO CHECK FILE EXISTENCE
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374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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375 */
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376
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377 def checkMetadataExists(file_path, msg) {
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378 file_path_obj = file( file_path )
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379
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380 if (msg.toString().find(/(?i)KMA/)) {
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381 if (!file_path_obj.parent.exists() || file_path_obj.parent.size() == 0) {
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382 stopNow("Please check if your ${msg}\n" +
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383 "[ ${file_path} ]\nexists and that the files are not of size 0.")
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384 }
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385 }
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386 else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
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387 stopNow("Please check if your ${msg} file\n" +
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388 "[ ${file_path} ]\nexists and is not of size 0.")
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389 }
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390 }
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391
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392 /*
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393 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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394 HELP TEXT METHODS FOR CRONOLOGY WORKFLOW
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395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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396 */
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397
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398 def help() {
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399
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400 Map helptext = [:]
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401 Map nH = [:]
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402 Map fastpAdapterHelp = [:]
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403 def uHelp = (params.help.getClass().toString() =~ /String/ ? params.help.tokenize(',').join(' ') : '')
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404
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405 Map defaultHelp = [
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406 '--help dpubmlstpy' : 'Show dl_pubmlst_profiles_and_schemes.py CLI options',
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407 '--help fastp' : 'Show fastp CLI options',
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408 '--help spades' : 'Show spades CLI options',
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409 '--help shovill' : 'Show shovill CLI options',
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410 '--help polypolish' : 'Show polypolish CLI options',
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411 '--help quast' : 'Show quast.py CLI options',
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412 '--help prodigal' : 'Show prodigal CLI options',
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413 '--help prokka' : 'Show prokka CLI options',
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414 '--help pirate' : 'Show priate CLI options',
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415 '--help mlst' : 'Show mlst CLI options',
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416 '--help mash' : 'Show mash `screen` CLI options',
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417 '--help tree' : 'Show mashtree CLI options',
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418 '--help abricate' : 'Show abricate CLI options\n'
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419 ]
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420
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421 fastpAdapterHelp['--fastp_use_custom_adapaters'] = "Use custom adapter FASTA with fastp on top of " +
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422 "built-in adapter sequence auto-detection. Enabling this option will attempt to find and remove " +
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423 "all possible Illumina adapter and primer sequences but will make the workflow run slow. " +
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424 "Default: ${params.fastp_use_custom_adapters}"
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425
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426 if (params.help.getClass().toString() =~ /Boolean/ || uHelp.size() == 0) {
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427 println conciseHelp('fastp,polypolish')
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428 helptext.putAll(defaultHelp)
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429 } else {
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430 params.help.tokenize(',').each { h ->
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431 if (defaultHelp.keySet().findAll{ it =~ /(?i)\b${h}\b/ }.size() == 0) {
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432 println conciseHelp('fastp,polypolish')
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433 stopNow("Tool [ ${h} ] is not a part of ${params.pipeline} pipeline.")
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434 }
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435 }
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436
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437 helptext.putAll(
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438 fastqEntryPointHelp() +
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439 (uHelp =~ /(?i)\bdpubmlstpy/ ? dpubmlstpyHelp(params).text : nH) +
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440 (uHelp =~ /(?i)\bfastp/ ? fastpHelp(params).text + fastpAdapterHelp : nH) +
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441 (uHelp =~ /(?i)\bmash/ ? mashscreenHelp(params).text : nH) +
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442 (uHelp =~ /(?i)\btuspy/ ? tuspyHelp(params).text : nH) +
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443 (uHelp =~ /(?i)\bspades/ ? spadesHelp(params).text : nH) +
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444 (uHelp =~ /(?i)\bshovill/ ? shovillHelp(params).text : nH) +
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445 (uHelp =~ /(?i)\bpolypolish/ ? polypolishHelp(params).text : nH) +
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446 (uHelp =~ /(?i)\bquast/ ? quastHelp(params).text : nH) +
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447 (uHelp =~ /(?i)\bprodigal/ ? prodigalHelp(params).text : nH) +
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448 (uHelp =~ /(?i)\bprokka/ ? prokkaHelp(params).text : nH) +
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449 (uHelp =~ /(?i)\bpirate/ ? pirateHelp(params).text : nH) +
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450 (uHelp =~ /(?i)\bmlst/ ? mlstHelp(params).text : nH) +
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451 (uHelp =~ /(?i)\btree/ ? mashtreeHelp(params).text : nH) +
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452 (uHelp =~ /(?i)\babricate/ ? abricateHelp(params).text : nH) +
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453 wrapUpHelp()
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454 )
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455 }
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456
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457 return addPadding(helptext)
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458 } |
