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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 java.util.zip.GZIPInputStream
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4 import java.io.FileInputStream
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5 import nextflow.file.FileHelper
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6
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7
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8 // Include any necessary methods
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9 include { \
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10 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
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11 addPadding; wrapUpHelp } from "${params.routines}"
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12 include { fastpHelp } from "${params.toolshelp}${params.fs}fastp"
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13 include { kmaalignHelp } from "${params.toolshelp}${params.fs}kmaalign"
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14 include { seqkitgrepHelp } from "${params.toolshelp}${params.fs}seqkitgrep"
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15 include { salmonidxHelp } from "${params.toolshelp}${params.fs}salmonidx"
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16 include { sourmashsketchHelp } from "${params.toolshelp}${params.fs}sourmashsketch"
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17 include { sourmashgatherHelp } from "${params.toolshelp}${params.fs}sourmashgather"
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18 include { sfhpyHelp } from "${params.toolshelp}${params.fs}sfhpy"
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19 include { gsalkronapyHelp } from "${params.toolshelp}${params.fs}gsalkronapy"
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20 include { kronaktimporttextHelp } from "${params.toolshelp}${params.fs}kronaktimporttext"
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21
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22 // Exit if help requested before any subworkflows
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23 if (params.help) {
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24 log.info help()
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25 exit 0
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26 }
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27
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28
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29 // Include any necessary modules and subworkflows
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30 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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31 include { FASTP } from "${params.modules}${params.fs}fastp${params.fs}main"
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32 include { KMA_ALIGN } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
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33 include { OTF_GENOME } from "${params.modules}${params.fs}otf_genome${params.fs}main"
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34 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
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35 include { SALMON_INDEX } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
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36 include { SALMON_QUANT } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
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37 include { SOURMASH_SKETCH } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
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38 include { SOURMASH_SKETCH \
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39 as REDUCE_DB_IDX } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
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40 include { SOURMASH_GATHER } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
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41 include { NOWAYOUT_RESULTS } from "${params.modules}${params.fs}nowayout_results${params.fs}main"
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42 include { KRONA_KTIMPORTTEXT } from "${params.modules}${params.fs}krona${params.fs}ktimporttext${params.fs}main"
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43 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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44 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
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45
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46 /*
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47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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48 INPUTS AND ANY CHECKS FOR THE NOWAYOUT WORKFLOW
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49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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50 */
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51
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52 def reads_platform = 0
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53 reads_platform += (params.input ? 1 : 0)
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54
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55 if (reads_platform < 1 || reads_platform == 0) {
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56 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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57 "FASTQ files sequenced using the --input option.\n" +
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58 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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59 }
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60
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61 params.fastp_adapter_fasta ? checkMetadataExists(params.fastp_adapter_fasta, 'Adapter sequences FASTA') : null
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62 checkMetadataExists(params.lineages_csv, 'Lineages CSV')
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63 checkMetadataExists(params.kmaalign_idx, 'KMA Indices')
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64 checkMetadataExists(params.ref_fna, 'FASTA reference')
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65
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66 ch_sourmash_lin = file( params.lineages_csv )
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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 RUN THE NOWAYOUT WORKFLOW
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72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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73 */
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74
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75 workflow NOWAYOUT {
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76 main:
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77 log.info summaryOfParams()
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78
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79 PROCESS_FASTQ()
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80
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81 PROCESS_FASTQ.out.versions
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82 .set { software_versions }
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83
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84 PROCESS_FASTQ.out.processed_reads
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85 .set { ch_processed_reads }
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86
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87 ch_processed_reads
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88 .map { meta, fastq ->
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89 meta.get_kma_hit_accs = true
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90 meta.salmon_decoys = params.dummyfile
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91 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
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92 meta.kma_t_db = params.kmaalign_idx
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93 [ meta, fastq ]
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94 }
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95 .filter { meta, fastq ->
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96 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
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97 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toAbsolutePath().toString() ) )
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98 fq_gzip.read() != -1
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99 }
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100 .set { ch_processed_reads }
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101
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102 FASTP( ch_processed_reads )
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103
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104 FASTP.out.json
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105 .map { meta, json ->
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106 json
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107 }
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108 .collect()
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109 .set { ch_multiqc }
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110
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111 KMA_ALIGN(
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112 FASTP.out.passed_reads
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113 .map { meta, fastq ->
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114 [meta, fastq, []]
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115 }
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116 )
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117
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118 OTF_GENOME(
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119 KMA_ALIGN.out.hits
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120 .join(KMA_ALIGN.out.frags)
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121 )
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122
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123 OTF_GENOME.out.reads_extracted
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124 .filter { meta, fasta ->
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125 fa_file = ( fasta.getClass().toString() =~ /ArrayList/ ? fasta : [ fasta ] )
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126 fa_gzip = new GZIPInputStream( new FileInputStream( fa_file[0].toAbsolutePath().toString() ) )
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127 fa_gzip.read() != -1
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128 }
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129 .set { ch_mito_aln_reads }
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130
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131 SEQKIT_GREP(
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132 KMA_ALIGN.out.hits
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133 .filter { meta, mapped_refs ->
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134 patterns = file( mapped_refs )
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135 patterns.size() > 0
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136 }
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137 .map { meta, mapped_refs ->
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138 [meta, params.ref_fna, mapped_refs]
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139 }
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140 )
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141
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142 SALMON_INDEX( SEQKIT_GREP.out.fastx )
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143
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144 SALMON_QUANT(
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145 ch_mito_aln_reads
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146 .join( SALMON_INDEX.out.idx )
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147 )
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148
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149 REDUCE_DB_IDX(
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150 SEQKIT_GREP.out.fastx,
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151 true,
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152 false,
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153 'db'
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154 )
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155
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156 SOURMASH_SKETCH(
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157 ch_mito_aln_reads,
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158 false,
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159 false,
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160 'query'
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161 )
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162
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163 SOURMASH_GATHER(
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164 SOURMASH_SKETCH.out.signatures
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165 .join( REDUCE_DB_IDX.out.signatures ),
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166 [], [], [], []
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167 )
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168
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169 // SOURMASH_TAX_METAGENOME(
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170 // SOURMASH_GATHER.out.result
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171 // .groupTuple(by: [0])
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172 // .map { meta, csv ->
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173 // [ meta, csv, ch_sourmash_lin ]
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174 // }
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175 // )
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176
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177 // SOURMASH_TAX_METAGENOME.out.csv
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178 // .map { meta, csv ->
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179 // csv
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180 // }
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181 // .set { ch_lin_csv }
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182
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183 // SOURMASH_TAX_METAGENOME.out.tsv
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184 // .tap { ch_lin_krona }
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185 // .map { meta, tsv ->
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186 // tsv
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187 // }
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188 // .tap { ch_lin_tsv }
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189
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190 SOURMASH_GATHER.out.result
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191 .groupTuple(by: [0])
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192 .map { meta, csv ->
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193 [ csv ]
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194 }
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195 .concat(
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196 SALMON_QUANT.out.results
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197 .map { meta, salmon_res ->
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198 [ salmon_res ]
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199 }
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200 )
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201 .concat(
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202 SOURMASH_GATHER.out.failed
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203 .map { meta, failed ->
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204 [ failed ]
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205 }
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206 )
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207 .concat( OTF_GENOME.out.failed )
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208 .collect()
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209 .flatten()
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210 .collect()
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211 .set { ch_gene_abn }
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212
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213 NOWAYOUT_RESULTS( ch_gene_abn, ch_sourmash_lin )
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214
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215 NOWAYOUT_RESULTS.out.tsv
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216 .flatten()
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217 .filter { tsv -> tsv.toString() =~ /.*${params.krona_res_suffix}$/ }
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218 .map { tsv ->
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219 meta = [:]
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220 meta.id = "${params.cfsanpipename}_${params.pipeline}_krona"
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221 [ meta, tsv ]
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222 }
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223 .groupTuple(by: [0])
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224 .set { ch_lin_krona }
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225
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226 // ch_lin_tsv
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227 // .mix( ch_lin_csv )
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228 // .collect()
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229 // .set { ch_lin_summary }
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230
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231 // SOURMASH_TAX_METAGENOME.out.txt
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232 // .map { meta, txt ->
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233 // txt
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234 // }
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235 // .collect()
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236 // .set { ch_lin_kreport }
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237
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238 // NOWAYOUT_RESULTS(
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239 // ch_lin_summary
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240 // .concat( SOURMASH_GATHER.out.failed )
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241 // .concat( OTF_GENOME.out.failed )
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242 // .collect()
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243 // )
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244
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245 KRONA_KTIMPORTTEXT( ch_lin_krona )
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246
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247 DUMP_SOFTWARE_VERSIONS(
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248 software_versions
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249 .mix (
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250 FASTP.out.versions,
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251 KMA_ALIGN.out.versions,
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252 SEQKIT_GREP.out.versions,
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253 REDUCE_DB_IDX.out.versions,
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254 SOURMASH_SKETCH.out.versions,
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255 SOURMASH_GATHER.out.versions,
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256 SALMON_INDEX.out.versions,
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257 SALMON_QUANT.out.versions,
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258 NOWAYOUT_RESULTS.out.versions,
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259 KRONA_KTIMPORTTEXT.out.versions
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260 )
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261 .unique()
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262 .collectFile(name: 'collected_versions.yml')
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263 )
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264
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265 DUMP_SOFTWARE_VERSIONS.out.mqc_yml
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266 .concat(
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267 ch_multiqc,
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268 NOWAYOUT_RESULTS.out.mqc_yml
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269 )
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270 .collect()
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271 .flatten()
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272 .collect()
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273 .set { ch_multiqc }
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274
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275 MULTIQC( ch_multiqc )
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276 }
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277
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278 /*
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279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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280 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
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281 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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282 */
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283
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284 workflow.onComplete {
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285 if (workflow.success) {
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286 sendMail()
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287 }
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288 }
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289
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290 workflow.onError {
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291 sendMail()
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292 }
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293
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294 /*
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295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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296 METHOD TO CHECK METADATA EXISTENCE
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297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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298 */
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299
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300 def checkMetadataExists(file_path, msg) {
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301 file_path_obj = file( file_path )
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302
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303 if (msg.toString().find(/(?i)KMA/)) {
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304 if (!file_path_obj.parent.exists()) {
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305 stopNow("Please check if your ${msg}\n" +
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306 "[ ${file_path} ]\nexists and that the files are not of size 0.")
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307 }
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308
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309 // Check if db files within parent path are empty.
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310 file_path_obj.parent.eachFileRecurse {
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311 if (it.size() == 0) {
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312 stopNow("For ${msg}, within\n" +
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313 "[ ${file_path} ],\nthe following file is of size 0: ${it.name}")
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314 }
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315 }
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316
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317 }
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318 else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
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319 stopNow("Please check if your ${msg} file\n" +
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320 "[ ${file_path} ]\nexists and is not of size 0.")
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321 }
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322 }
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323
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324 /*
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325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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326 HELP TEXT METHODS FOR NOWAYOUT WORKFLOW
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327 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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328 */
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329
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330 def help() {
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331
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332 Map helptext = [:]
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333
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334 helptext.putAll (
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335 fastqEntryPointHelp() +
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336 fastpHelp(params).text +
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337 kmaalignHelp(params).text +
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338 seqkitgrepHelp(params).text +
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339 salmonidxHelp(params).text +
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340 sourmashsketchHelp(params).text +
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341 sourmashgatherHelp(params).text +
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342 sfhpyHelp(params).text +
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343 gsalkronapyHelp(params).text +
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344 kronaktimporttextHelp(params).text +
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345 wrapUpHelp()
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346 )
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347
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348 return addPadding(helptext)
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349 }
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