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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; conciseHelp; \
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11 addPadding; wrapUpHelp } from "${params.routines}"
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12 include { bbmergeHelp } from "${params.toolshelp}${params.fs}bbmerge"
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13 include { fastpHelp } from "${params.toolshelp}${params.fs}fastp"
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14 include { mashscreenHelp } from "${params.toolshelp}${params.fs}mashscreen"
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15 include { tuspyHelp } from "${params.toolshelp}${params.fs}tuspy"
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16 include { sourmashsketchHelp } from "${params.toolshelp}${params.fs}sourmashsketch"
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17 include { sourmashgatherHelp } from "${params.toolshelp}${params.fs}sourmashgather"
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18 include { sourmashsearchHelp } from "${params.toolshelp}${params.fs}sourmashsearch"
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19 include { sfhpyHelp } from "${params.toolshelp}${params.fs}sfhpy"
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20 include { kmaindexHelp } from "${params.toolshelp}${params.fs}kmaindex"
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21 include { kmaalignHelp } from "${params.toolshelp}${params.fs}kmaalign"
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22 include { megahitHelp } from "${params.toolshelp}${params.fs}megahit"
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23 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
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24 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
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25 include { salmonidxHelp } from "${params.toolshelp}${params.fs}salmonidx"
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26 include { gsrpyHelp } from "${params.toolshelp}${params.fs}gsrpy"
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27
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28 // Exit if help requested before any subworkflows
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29 if (params.help) {
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30 log.info help()
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31 exit 0
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32 }
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33
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34
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35 // Include any necessary modules and subworkflows
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36 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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37 include { CAT_CAT } from "${params.modules}${params.fs}cat_cat${params.fs}main"
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38 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
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39 include { BBTOOLS_BBMERGE } from "${params.modules}${params.fs}bbtools${params.fs}bbmerge${params.fs}main"
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40 include { FASTP } from "${params.modules}${params.fs}fastp${params.fs}main"
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41 include { MASH_SCREEN } from "${params.modules}${params.fs}mash${params.fs}screen${params.fs}main"
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42 include { TOP_UNIQUE_SEROVARS } from "${params.modules}${params.fs}top_unique_serovars${params.fs}main"
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43 include { SOURMASH_SKETCH } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
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44 include { SOURMASH_GATHER } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
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45 include { SOURMASH_SEARCH } from "${params.modules}${params.fs}sourmash${params.fs}search${params.fs}main"
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46 include { KMA_INDEX } from "${params.modules}${params.fs}kma${params.fs}index${params.fs}main"
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47 include { KMA_ALIGN } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
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48 include { OTF_GENOME } from "${params.modules}${params.fs}otf_genome${params.fs}main"
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49 include { MEGAHIT_ASSEMBLE } from "${params.modules}${params.fs}megahit${params.fs}assemble${params.fs}main"
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50 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
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51 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
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52 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
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53 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
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54 include { SALMON_INDEX } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
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55 include { SALMON_QUANT } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
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56 include { SOURMASH_COMPARE } from "${params.modules}${params.fs}custom${params.fs}sourmash${params.fs}compare${params.fs}main"
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57 include { BCS_DISTANCE_MATRIX } from "${params.modules}${params.fs}bcs_distance_matrix${params.fs}main"
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58 include { BCS_RESULTS } from "${params.modules}${params.fs}bcs_results${params.fs}main"
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59 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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60 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
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61
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62 /*
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63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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64 INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
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65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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66 */
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67
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68 def reads_platform = 0
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69 def salmon_idx_decoys = file ( "${params.salmonidx_decoys}" )
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70 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
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71
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72 reads_platform += (params.input ? 1 : 0)
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73
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74 if (reads_platform < 1 || reads_platform == 0) {
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75 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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76 "FASTQ files sequenced using the --input option.\n" +
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77 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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78 }
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79
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80 checkMetadataExists(params.mash_sketch, 'MASH sketch')
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81 checkMetadataExists(params.tuspy_ps, 'ACC2SERO pickle')
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82 checkMetadataExists(params.gsrpy_snp_clus_metadata, 'PDG reference target cluster metadata')
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83
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84 /*
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85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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86 RUN THE BETTERCALLSAL WORKFLOW
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87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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88 */
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89
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90 workflow BETTERCALLSAL {
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91 main:
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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
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96 PROCESS_FASTQ
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97 .out
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98 .versions
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99 .set { software_versions }
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100
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101 PROCESS_FASTQ
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102 .out
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103 .processed_reads
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104 .set { ch_processed_reads }
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105
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106 if (params.bbmerge_run && !params.fq_single_end) {
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107 ch_processed_reads
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108 .map { meta, fastq ->
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109 meta.adapters = (params.bbmerge_adapters ?: params.dummyfile)
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110 [ meta, fastq ]
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111 }
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112 .set { ch_processed_reads }
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113
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114 BBTOOLS_BBMERGE( ch_processed_reads )
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115
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116 BBTOOLS_BBMERGE
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117 .out
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118 .fastq
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119 .map { meta, fastq -> [ meta, [ fastq ] ] }
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120 .set { ch_processed_reads }
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121
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122 software_versions
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123 .mix ( BBTOOLS_BBMERGE.out.versions )
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124 .set { software_versions }
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125 }
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126
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127 if (params.fastp_run) {
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128 FASTP ( ch_processed_reads )
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129
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130 FASTP
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131 .out
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132 .passed_reads
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133 .set { ch_processed_reads }
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134
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135 FASTP
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136 .out
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137 .json
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138 .map { meta, json -> [ json ] }
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139 .collect()
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140 .set { ch_multiqc }
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141
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142 software_versions
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143 .mix ( FASTP.out.versions )
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144 .set { software_versions }
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145 } else {
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146 FASTQC ( ch_processed_reads )
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147
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148 FASTQC
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149 .out
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150 .zip
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151 .map { meta, zip -> [ zip ] }
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152 .collect()
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153 .set { ch_multiqc }
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154
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155 software_versions
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156 .mix ( FASTQC.out.versions )
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157 .set { software_versions }
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158 }
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159
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160 if (params.bcs_concat_pe && !params.fq_single_end && !params.bbmerge_run) {
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161 CAT_CAT ( ch_processed_reads )
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162
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163 CAT_CAT
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164 .out
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165 .concatenated_reads
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166 .set { ch_processed_reads }
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167
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168 software_versions
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169 .mix ( CAT_CAT.out.versions )
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170 .set { software_versions }
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171 }
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172
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173 ch_processed_reads
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174 .map { meta, fastq ->
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175 meta.sequence_sketch = params.mash_sketch
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176 meta.get_kma_hit_accs = true
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177 meta.single_end = true
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178 meta.salmon_decoys = params.dummyfile
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179 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
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180 [ meta, fastq ]
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181 }
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182 .filter { meta, fastq ->
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183 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
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184 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toString() ) )
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185 fq_gzip.read() != -1
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186 }
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187 .set { ch_processed_reads }
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188
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189 MASH_SCREEN ( ch_processed_reads )
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190
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191 TOP_UNIQUE_SEROVARS ( MASH_SCREEN.out.screened )
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192
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193 TOP_UNIQUE_SEROVARS.out.genomes_fasta
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194 .set { ch_genomes_fasta }
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195
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196 TOP_UNIQUE_SEROVARS.out.failed
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197 .set { ch_bcs_calls_failed }
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198
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199 if (params.sourmashgather_run || params.sourmashsearch_run) {
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200 SOURMASH_SKETCH (
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201 ch_processed_reads
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202 .join ( ch_genomes_fasta )
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203 )
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204
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205 if (params.sourmashgather_run) {
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206 SOURMASH_GATHER (
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207 SOURMASH_SKETCH.out.signatures,
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208 [], [], [], []
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209 )
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210
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211 SOURMASH_GATHER
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212 .out
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213 .genomes_fasta
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214 .set { ch_genomes_fasta }
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215
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216 ch_bcs_calls_failed
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217 .concat ( SOURMASH_GATHER.out.failed )
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218 .set { ch_bcs_calls_failed }
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219
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220 software_versions
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221 .mix ( SOURMASH_GATHER.out.versions.ifEmpty(null) )
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222 .set { software_versions }
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223 }
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224
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225 if (params.sourmashsearch_run) {
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226 SOURMASH_SEARCH (
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227 SOURMASH_SKETCH.out.signatures,
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228 []
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229 )
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230
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231 SOURMASH_SEARCH
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232 .out
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233 .genomes_fasta
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234 .set { ch_genomes_fasta }
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235
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236 ch_bcs_calls_failed
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237 .concat ( SOURMASH_SEARCH.out.failed )
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238 .set { ch_bcs_calls_failed }
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239
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240 software_versions
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241 .mix ( SOURMASH_SEARCH.out.versions.ifEmpty(null) )
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242 .set { software_versions }
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243 }
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244 }
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245
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246 KMA_INDEX ( ch_genomes_fasta )
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247
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248 KMA_ALIGN (
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249 ch_processed_reads
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250 .join ( KMA_INDEX.out.idx )
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251 )
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252
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253 OTF_GENOME (
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254 KMA_ALIGN.out.hits
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255 .join ( KMA_ALIGN.out.frags )
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256 )
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257
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258 OTF_GENOME.out.failed
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259 .concat ( ch_bcs_calls_failed )
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260 .collectFile( name: 'BCS_NO_CALLS.txt' )
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261 .set { ch_bcs_no_calls }
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262
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263 SALMON_INDEX ( OTF_GENOME.out.genomes_fasta )
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264
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265 SALMON_QUANT (
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266 ch_processed_reads
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267 .join ( SALMON_INDEX.out.idx )
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268 )
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269
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270 SALMON_QUANT
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271 .out
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272 .results
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273 .groupTuple(by: [0])
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274 .map { it -> tuple ( it[1].flatten() ) }
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275 .mix ( ch_bcs_no_calls )
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276 .collect()
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277 .set { ch_salmon_res_dirs }
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278
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279 if (params.sourmashsketch_run) {
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280 SOURMASH_SKETCH
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281 .out
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282 .signatures
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283 .groupTuple(by: [0])
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284 .map { meta, qsigs, dsigs -> [ qsigs ] }
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285 .collect()
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286 .flatten()
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287 .collect()
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288 .set { ch_query_sigs }
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289
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290 KMA_ALIGN
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291 .out
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292 .hits
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293 .map { meta, hits -> [ hits ] }
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294 .collect()
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295 .flatten()
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296 .collectFile(name: 'accessions.txt')
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297 .set { ch_otf_genomes }
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298
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299 if (params.megahit_run) {
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300
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301 MEGAHIT_ASSEMBLE ( OTF_GENOME.out.reads_extracted )
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302
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303 MEGAHIT_ASSEMBLE
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304 .out
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305 .assembly
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306 .set { ch_asm_filtered_contigs }
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307
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308 MLST ( ch_asm_filtered_contigs )
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309
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310 MLST.out.tsv
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311 .map { meta, tsv -> [ 'mlst', tsv] }
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312 .groupTuple(by: [0])
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313 .map { it -> tuple ( it[0], it[1].flatten() ) }
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314 .set { ch_mqc_custom_tbl }
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315
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316 ABRICATE_RUN (
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317 ch_asm_filtered_contigs,
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318 abricate_dbs
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319 )
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320
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321 ABRICATE_RUN
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322 .out
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323 .abricated
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324 .map { meta, abres -> [ abricate_dbs, abres ] }
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325 .groupTuple(by: [0])
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326 .map { it -> tuple ( it[0], it[1].flatten() ) }
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327 .set { ch_abricated }
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328
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329 ABRICATE_SUMMARY ( ch_abricated )
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330
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331 ch_mqc_custom_tbl
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332 .concat (
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333 ABRICATE_SUMMARY.out.ncbiamrplus.map { it -> tuple ( it[0], it[1] )},
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334 ABRICATE_SUMMARY.out.resfinder.map { it -> tuple ( it[0], it[1] )},
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335 ABRICATE_SUMMARY.out.megares.map { it -> tuple ( it[0], it[1] )},
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336 ABRICATE_SUMMARY.out.argannot.map { it -> tuple ( it[0], it[1] )},
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337 )
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338 .groupTuple(by: [0])
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339 .map { it -> [ it[0], it[1].flatten() ]}
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340 .set { ch_mqc_custom_tbl }
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341
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342 TABLE_SUMMARY ( ch_mqc_custom_tbl )
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343
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344 ch_multiqc
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345 .concat ( TABLE_SUMMARY.out.mqc_yml )
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346 .set { ch_multiqc }
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347
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348 software_versions
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349 .mix (
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350 MEGAHIT_ASSEMBLE.out.versions.ifEmpty(null),
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351 MLST.out.versions.ifEmpty(null),
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352 ABRICATE_RUN.out.versions.ifEmpty(null),
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353 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
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354 TABLE_SUMMARY.out.versions.ifEmpty(null)
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355 )
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356 .set { software_versions }
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357 }
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358
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359 SOURMASH_COMPARE ( ch_query_sigs, ch_otf_genomes )
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360
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361 BCS_DISTANCE_MATRIX (
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362 SOURMASH_COMPARE.out.matrix,
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363 SOURMASH_COMPARE.out.labels
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364 )
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365
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366 ch_multiqc
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367 .concat ( BCS_DISTANCE_MATRIX.out.mqc_yml )
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368 .set { ch_multiqc }
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369
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370 software_versions
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371 .mix (
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372 SOURMASH_SKETCH.out.versions.ifEmpty(null),
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373 SOURMASH_COMPARE.out.versions.ifEmpty(null),
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374 BCS_DISTANCE_MATRIX.out.versions.ifEmpty(null),
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375 )
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376 .set { software_versions }
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377 }
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378
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379 BCS_RESULTS ( ch_salmon_res_dirs )
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380
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381 DUMP_SOFTWARE_VERSIONS (
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382 software_versions
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383 .mix (
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384 MASH_SCREEN.out.versions,
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385 TOP_UNIQUE_SEROVARS.out.versions,
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386 KMA_INDEX.out.versions,
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387 KMA_ALIGN.out.versions,
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388 OTF_GENOME.out.versions.ifEmpty(null),
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389 SALMON_INDEX.out.versions,
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390 SALMON_QUANT.out.versions,
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391 BCS_RESULTS.out.versions
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392 )
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393 .unique()
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394 .collectFile(name: 'collected_versions.yml')
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395 )
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396
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397 if (params.multiqc_run) {
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398 DUMP_SOFTWARE_VERSIONS
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399 .out
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400 .mqc_yml
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401 .concat (
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402 ch_multiqc,
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403 BCS_RESULTS.out.mqc_yml,
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404 BCS_RESULTS.out.mqc_json
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405 )
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406 .collect()
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407 .set { ch_multiqc }
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408
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409 MULTIQC ( ch_multiqc )
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410 }
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411
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412 }
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413
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414 /*
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415 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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416 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
|
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417 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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418 */
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419
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420 workflow.onComplete {
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421 if (workflow.success) {
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422 sendMail()
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423 }
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424 }
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425
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426 workflow.onError {
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427 sendMail()
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428 }
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429
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430 /*
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431 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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432 METHOD TO CHECK METADATA EXISTENCE
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433 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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434 */
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435
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436 def checkMetadataExists(file_path, msg) {
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437 file_path_obj = file( file_path )
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438
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439 if (!file_path_obj.exists() || file_path_obj.size() == 0) {
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440 stopNow("Please check if your ${msg} file\n" +
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441 "[ ${file_path} ]\nexists and is not of size 0.")
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442 }
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443 }
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444
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445 /*
|
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446 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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447 HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
|
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448 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
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449 */
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450
|
|
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451 def help() {
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452
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453 Map helptext = [:]
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454 Map bcsConcatHelp = [:]
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455 Map fastpAdapterHelp = [:]
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456 Map nH = [:]
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457 def uHelp = (params.help.getClass().toString() =~ /String/ ? params.help.tokenize(',').join(' ') : '')
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458
|
|
|
459 Map defaultHelp = [
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|
460 '--help bbmerge' : 'Show bbmerge.sh CLI options',
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|
461 '--help fastp' : 'Show fastp CLI options',
|
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462 '--help mash' : 'Show mash `screen` CLI options',
|
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|
463 '--help tuspy' : 'Show get_top_unique_mash_hit_genomes.py CLI options',
|
|
|
464 '--help sourmashsketch' : 'Show sourmash `sketch` CLI options',
|
|
|
465 '--help sourmashgather' : 'Show sourmash `gather` CLI options',
|
|
|
466 '--help sourmashsearch' : 'Show sourmash `search` CLI options',
|
|
|
467 '--help sfhpy' : 'Show sourmash_filter_hits.py CLI options',
|
|
|
468 '--help kmaindex' : 'Show kma `index` CLI options',
|
|
|
469 '--help kmaalign' : 'Show kma CLI options',
|
|
|
470 '--help megahit' : 'Show megahit CLI options',
|
|
|
471 '--help mlst' : 'Show mlst CLI options',
|
|
|
472 '--help abricate' : 'Show abricate CLI options',
|
|
|
473 '--help salmon' : 'Show salmon `index` CLI options',
|
|
|
474 '--help gsrpy' : 'Show gen_salmon_res_table.py CLI options\n'
|
|
|
475 ]
|
|
|
476
|
|
|
477 bcsConcatHelp['--bcs_concat_pe'] = "Concatenate paired-end files. " +
|
|
|
478 "Default: ${params.bcs_concat_pe}"
|
|
|
479
|
|
|
480 fastpAdapterHelp['--fastp_use_custom_adapaters'] = "Use custom adapter FASTA with fastp on top of " +
|
|
|
481 "built-in adapter sequence auto-detection. Enabling this option will attempt to find and remove " +
|
|
|
482 "all possible Illumina adapter and primer sequences but will make the workflow run slow. " +
|
|
|
483 "Default: ${params.fastp_use_custom_adapters}"
|
|
|
484
|
|
|
485 if (params.help.getClass().toString() =~ /Boolean/ || uHelp.size() == 0) {
|
|
|
486 println conciseHelp('fastp,mash')
|
|
|
487 helptext.putAll(defaultHelp)
|
|
|
488 } else {
|
|
|
489 params.help.tokenize(',').each { h ->
|
|
|
490 if (defaultHelp.keySet().findAll{ it =~ /(?i)\b${h}\b/ }.size() == 0) {
|
|
|
491 println conciseHelp('fastp,mash')
|
|
|
492 stopNow("Tool [ ${h} ] is not a part of ${params.pipeline} pipeline.")
|
|
|
493 }
|
|
|
494 }
|
|
|
495
|
|
|
496 helptext.putAll(
|
|
|
497 fastqEntryPointHelp() +
|
|
|
498 bcsConcatHelp +
|
|
|
499 (uHelp =~ /(?i)\bbbmerge/ ? bbmergeHelp(params).text : nH) +
|
|
|
500 (uHelp =~ /(?i)\bfastp/ ? fastpHelp(params).text + fastpAdapterHelp : nH) +
|
|
|
501 (uHelp =~ /(?i)\bmash/ ? mashscreenHelp(params).text : nH) +
|
|
|
502 (uHelp =~ /(?i)\btuspy/ ? tuspyHelp(params).text : nH) +
|
|
|
503 (uHelp =~ /(?i)\bsourmashsketch/ ? sourmashsketchHelp(params).text : nH) +
|
|
|
504 (uHelp =~ /(?i)\bsourmashgather/ ? sourmashgatherHelp(params).text : nH) +
|
|
|
505 (uHelp =~ /(?i)\bsourmashsearch/ ? sourmashsearchHelp(params).text : nH) +
|
|
|
506 (uHelp =~ /(?i)\bsfhpy/ ? sfhpyHelp(params).text : nH) +
|
|
|
507 (uHelp =~ /(?i)\bkmaindex/ ? kmaindexHelp(params).text : nH) +
|
|
|
508 (uHelp =~ /(?i)\bkmaalign/ ? kmaalignHelp(params).text : nH) +
|
|
|
509 (uHelp =~ /(?i)\bmegahit/ ? megahitHelp(params).text : nH) +
|
|
|
510 (uHelp =~ /(?i)\bmlst/ ? mlstHelp(params).text : nH) +
|
|
|
511 (uHelp =~ /(?i)\babricate/ ? abricateHelp(params).text : nH) +
|
|
|
512 (uHelp =~ /(?i)\bsalmon/ ? salmonidxHelp(params).text : nH) +
|
|
|
513 (uHelp =~ /(?i)\bgsrpy/ ? gsrpyHelp(params).text : nH) +
|
|
|
514 wrapUpHelp()
|
|
|
515 )
|
|
|
516 }
|
|
|
517
|
|
|
518 return addPadding(helptext)
|
|
|
519 } |
