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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 "${params.routines}"
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12 include { filtlongHelp } from "${params.toolshelp}${params.fs}filtlong"
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13 include { mashscreenHelp } from "${params.toolshelp}${params.fs}mashscreen"
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14 include { tuspyHelp } from "${params.toolshelp}${params.fs}tuspy"
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15 include { sourmashsketchHelp } from "${params.toolshelp}${params.fs}sourmashsketch"
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16 include { sourmashgatherHelp } from "${params.toolshelp}${params.fs}sourmashgather"
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17 include { sourmashsearchHelp } from "${params.toolshelp}${params.fs}sourmashsearch"
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18 include { sfhpyHelp } from "${params.toolshelp}${params.fs}sfhpy"
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19 include { flyeHelp } from "${params.toolshelp}${params.fs}flye"
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20 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
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21 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
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22 include { gsrpyHelp } from "${params.toolshelp}${params.fs}gsrpy"
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23
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24 // Exit if help requested before any subworkflows
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25 if (params.help) {
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26 log.info help()
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27 exit 0
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28 }
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29
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30
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31 // Include any necessary modules and subworkflows
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32 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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33 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
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34 include { FILTLONG } from "${params.modules}${params.fs}filtlong${params.fs}main"
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35 include { MASH_SCREEN } from "${params.modules}${params.fs}mash${params.fs}screen${params.fs}main"
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36 include { TOP_UNIQUE_SEROVARS } from "${params.modules}${params.fs}top_unique_serovars${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_GATHER } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
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39 include { SOURMASH_SEARCH } from "${params.modules}${params.fs}sourmash${params.fs}search${params.fs}main"
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40 include { GATHER_HITS } from "${params.modules}${params.fs}gather_hits${params.fs}main"
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41 include { OTF_GENOME } from "${params.modules}${params.fs}otf_genome${params.fs}main"
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42 include { FLYE_ASSEMBLE } from "${params.modules}${params.fs}flye${params.fs}assemble${params.fs}main"
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43 include { MINIMAP2_ALIGN } from "${params.modules}${params.fs}minimap2${params.fs}align${params.fs}main"
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44 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
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45 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
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46 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
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47 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
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48 include { SALMON_QUANT } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
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49 include { SOURMASH_COMPARE } from "${params.modules}${params.fs}custom${params.fs}sourmash${params.fs}compare${params.fs}main"
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50 include { BCS_DISTANCE_MATRIX } from "${params.modules}${params.fs}bcs_distance_matrix${params.fs}main"
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51 include { BCS_RESULTS } from "${params.modules}${params.fs}bcs_results${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 BETTERCALLSAL WORKFLOW
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58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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59 */
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60
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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 (reads_platform < 1 || reads_platform == 0) {
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67 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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68 "FASTQ files sequenced using the --input option.\n" +
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69 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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70 }
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71
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72 checkMetadataExists(params.mash_sketch, 'MASH sketch')
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73 checkMetadataExists(params.tuspy_ps, 'ACC2SERO pickle')
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74 checkMetadataExists(params.gsrpy_snp_clus_metadata, 'PDG reference target cluster metadata')
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75
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76 /*
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77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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78 RUN THE BETTERCALLSAL_LR WORKFLOW
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79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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80 */
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81
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82 workflow BETTERCALLSAL_LR {
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83 main:
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84 log.info summaryOfParams()
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85
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86 aaaa = Channel.empty()
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87
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88 PROCESS_FASTQ()
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89
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90 PROCESS_FASTQ.out.versions
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91 .set { software_versions }
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92
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93 PROCESS_FASTQ.out.processed_reads
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94 .tap { ch_fpass_processed_reads }
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95 .map { meta, fastq ->
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96 meta.single_end = params.fq_single_end
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97 [ meta, [], fastq ]
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98 }
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99 .set { ch_processed_reads_lr }
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100
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101 FILTLONG ( ch_processed_reads_lr )
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102
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103 FILTLONG.out.filtered_reads
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104 .map { meta, fastq ->
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105 def meta2 = [:]
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106 meta2.id = meta.id.toString() + '.filtered'
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107 meta2.single_end = meta.single_end
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108 meta2.strandedness = meta.strandedness
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109 [ meta2, fastq ]
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110 }
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111 .set { ch_processed_reads_fqc }
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112
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113 FILTLONG.out.log
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114 .map { meta, log -> [ log ] }
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115 .collect()
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116 .set { ch_multiqc }
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117
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118 FASTQC (
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119 ch_fpass_processed_reads
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120 .map { meta, fastq ->
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121 def meta2 = [:]
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122 meta2.id = meta.id.toString() + '.raw'
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123 meta2.single_end = meta.single_end
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124 meta2.strandedness = meta.strandedness
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125 [ meta2, fastq ]
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126 }
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127 .concat ( ch_processed_reads_fqc )
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128 )
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129
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130 FASTQC.out.zip
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131 .map { meta, zip -> [ zip ] }
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132 .collect()
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133 .set { ch_fqc_mqc }
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134
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135 FILTLONG.out.filtered_reads
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136 .map { meta, fastq ->
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137 meta.sequence_sketch = params.mash_sketch
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138 meta.single_end = true
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139 meta.salmon_alignment_mode = true
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140 meta.salmon_decoys = params.dummyfile
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141 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
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142 [ meta, fastq ]
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143 }
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144 .filter { meta, fastq ->
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145 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
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146 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toString() ) )
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147 fq_gzip.read() != -1
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148 }
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149 .set { ch_processed_reads }
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150
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151 MASH_SCREEN ( ch_processed_reads )
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152
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153 TOP_UNIQUE_SEROVARS ( MASH_SCREEN.out.screened )
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154
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155 TOP_UNIQUE_SEROVARS.out.genomes_fasta
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156 .set { ch_genomes_fasta }
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157
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158 TOP_UNIQUE_SEROVARS.out.failed
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159 .set { ch_bcs_calls_failed }
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160
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161 if (params.sourmashgather_run || params.sourmashsearch_run) {
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162 SOURMASH_SKETCH (
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163 ch_processed_reads
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164 .join ( ch_genomes_fasta )
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165 )
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166
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167 if (params.sourmashgather_run) {
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168 SOURMASH_GATHER (
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169 SOURMASH_SKETCH.out.signatures,
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170 [], [], [], []
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171 )
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172
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173 SOURMASH_GATHER.out.genomes_fasta
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174 .set { ch_genomes_fasta }
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175
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176 ch_bcs_calls_failed
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177 .concat ( SOURMASH_GATHER.out.failed )
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178 .set { ch_bcs_calls_failed }
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179
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180 software_versions
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181 .mix ( SOURMASH_GATHER.out.versions.ifEmpty(null) )
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182 .set { software_versions }
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183 }
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184
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185 if (params.sourmashsearch_run) {
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186 SOURMASH_SEARCH (
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187 SOURMASH_SKETCH.out.signatures,
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188 []
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189 )
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190
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191 SOURMASH_SEARCH.out.genomes_fasta
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192 .set { ch_genomes_fasta }
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193
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194 ch_bcs_calls_failed
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195 .concat ( SOURMASH_SEARCH.out.failed )
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196 .set { ch_bcs_calls_failed }
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197
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198 software_versions
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199 .mix ( SOURMASH_SEARCH.out.versions.ifEmpty(null) )
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200 .set { software_versions }
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201 }
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202 }
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203
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204 GATHER_HITS ( ch_genomes_fasta )
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205
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206 OTF_GENOME (
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207 GATHER_HITS.out.sm_template_hits
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208 .map { meta, hits ->
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209 [meta, hits, []]
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210 }
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211 )
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212
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213 OTF_GENOME.out.failed
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214 .concat ( ch_bcs_calls_failed )
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215 .collectFile( name: 'BCS_NO_CALLS.txt' )
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216 .set { ch_bcs_no_calls }
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217
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218 OTF_GENOME.out.genomes_fasta
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219 .join ( ch_processed_reads )
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220 .multiMap { meta, genomes, filtered ->
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221 reads: [meta, filtered]
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222 assmb: [meta, genomes]
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223 }
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224 .set { ch_assemble_these }
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225
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226 MINIMAP2_ALIGN (
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227 ch_assemble_these.reads,
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228 ch_assemble_these.assmb,
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229 params.mm2_align_bam,
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230 params.mm2_align_bam_sorted,
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231 params.mm2_align_cigar_paf,
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232 params.mm2_align_cigar_bam
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233 )
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234
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235 SALMON_QUANT (
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236 MINIMAP2_ALIGN.out.bam
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237 .join ( ch_assemble_these.assmb )
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238 )
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239
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240 SALMON_QUANT.out.results
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241 .groupTuple(by: [0])
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242 .map { it -> tuple ( it[1].flatten() ) }
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243 .mix ( ch_bcs_no_calls )
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244 .collect()
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245 .set { ch_salmon_res_dirs }
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246
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247 if (params.sourmashsketch_run) {
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248 SOURMASH_SKETCH.out.signatures
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249 .groupTuple(by: [0])
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250 .map { meta, qsigs, dsigs -> [ qsigs ] }
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251 .collect()
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252 .flatten()
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253 .collect()
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254 .set { ch_query_sigs }
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255
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256 GATHER_HITS.out.sm_template_hits
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257 .map { meta, hits -> [ hits ] }
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258 .collect()
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259 .flatten()
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260 .collectFile(name: 'accessions.txt')
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261 .set { ch_otf_genomes }
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262
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263 if (params.flye_run) {
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264
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265 FLYE_ASSEMBLE ( ch_assemble_these.reads )
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266
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267 FLYE_ASSEMBLE.out.assembly
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268 .set { ch_asm_polished_contigs }
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269
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270 MLST ( ch_asm_polished_contigs )
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271
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272 MLST.out.tsv
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273 .map { meta, tsv -> [ 'mlst', tsv] }
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274 .groupTuple(by: [0])
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275 .map { it -> tuple ( it[0], it[1].flatten() ) }
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276 .set { ch_mqc_custom_tbl }
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277
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278 ABRICATE_RUN (
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279 ch_asm_polished_contigs,
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280 abricate_dbs
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281 )
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282
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283 ABRICATE_RUN.out.abricated
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284 .map { meta, abres -> [ abricate_dbs, abres ] }
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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_abricated }
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288
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289 ABRICATE_SUMMARY ( ch_abricated )
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290
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291 ch_mqc_custom_tbl
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292 .concat (
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293 ABRICATE_SUMMARY.out.ncbiamrplus.map { it -> tuple ( it[0], it[1] )},
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294 ABRICATE_SUMMARY.out.resfinder.map { it -> tuple ( it[0], it[1] )},
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295 ABRICATE_SUMMARY.out.megares.map { it -> tuple ( it[0], it[1] )},
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296 ABRICATE_SUMMARY.out.argannot.map { it -> tuple ( it[0], it[1] )},
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297 )
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298 .groupTuple(by: [0])
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299 .map { it -> [ it[0], it[1].flatten() ]}
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300 .set { ch_mqc_custom_tbl }
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301
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302 TABLE_SUMMARY ( ch_mqc_custom_tbl )
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303
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304 ch_multiqc
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305 .concat ( TABLE_SUMMARY.out.mqc_yml )
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306 .set { ch_multiqc }
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307
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308 software_versions
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309 .mix (
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310 FLYE_ASSEMBLE.out.versions.ifEmpty(null),
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311 MLST.out.versions.ifEmpty(null),
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312 ABRICATE_RUN.out.versions.ifEmpty(null),
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313 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
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314 TABLE_SUMMARY.out.versions.ifEmpty(null)
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315 )
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316 .set { software_versions }
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317 }
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318
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319 SOURMASH_COMPARE ( ch_query_sigs, ch_otf_genomes )
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320
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321 BCS_DISTANCE_MATRIX (
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322 SOURMASH_COMPARE.out.matrix,
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323 SOURMASH_COMPARE.out.labels
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324 )
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325
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326 ch_multiqc
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327 .concat ( BCS_DISTANCE_MATRIX.out.mqc_yml )
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328 .set { ch_multiqc }
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329
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330 software_versions
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331 .mix (
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332 SOURMASH_SKETCH.out.versions.ifEmpty(null),
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333 SOURMASH_COMPARE.out.versions.ifEmpty(null),
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334 BCS_DISTANCE_MATRIX.out.versions.ifEmpty(null),
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335 )
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336 .set { software_versions }
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337 }
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338
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339 BCS_RESULTS ( ch_salmon_res_dirs )
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340
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341 DUMP_SOFTWARE_VERSIONS (
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342 software_versions
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343 .mix (
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344 FILTLONG.out.versions,
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345 FASTQC.out.versions,
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346 MASH_SCREEN.out.versions,
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347 TOP_UNIQUE_SEROVARS.out.versions,
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348 GATHER_HITS.out.versions,
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349 OTF_GENOME.out.versions.ifEmpty(null),
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350 MINIMAP2_ALIGN.out.versions,
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351 SALMON_QUANT.out.versions,
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352 BCS_RESULTS.out.versions
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353 )
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354 .unique()
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355 .collectFile(name: 'collected_versions.yml')
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356 )
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357
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358 if (params.multiqc_run) {
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359 DUMP_SOFTWARE_VERSIONS.out.mqc_yml
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360 .concat (
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361 ch_multiqc,
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362 ch_fqc_mqc,
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363 BCS_RESULTS.out.mqc_yml,
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364 BCS_RESULTS.out.mqc_json
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365 )
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366 .collect()
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367 .set { ch_multiqc }
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368
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369 MULTIQC ( ch_multiqc )
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370 }
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371
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372 }
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373
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374 /*
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375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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376 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
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377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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378 */
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379
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380 workflow.onComplete {
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381 if (workflow.success) {
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382 sendMail()
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383 }
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384 }
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385
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386 workflow.onError {
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387 sendMail()
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388 }
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389
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390 /*
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391 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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392 METHOD TO CHECK METADATA EXISTENCE
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393 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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394 */
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395
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396 def checkMetadataExists(file_path, msg) {
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397 file_path_obj = file( file_path )
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398
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399 if (!file_path_obj.exists() || file_path_obj.size() == 0) {
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400 stopNow("Please check if your ${msg} file\n" +
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401 "[ ${file_path} ]\nexists and is not of size 0.")
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402 }
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403 }
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404
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405 /*
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406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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407 HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
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408 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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409 */
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410
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411 def help() {
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412
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413 Map helptext = [:]
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414 Map nH = [:]
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415 def uHelp = (params.help.getClass().toString() =~ /String/ ? params.help.tokenize(',').join(' ') : '')
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416
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417 Map defaultHelp = [
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418 '--help filtlong' : 'Show filtlong CLI options',
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419 '--help mash' : 'Show mash `screen` CLI options',
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420 '--help tuspy' : 'Show get_top_unique_mash_hit_genomes.py CLI options',
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421 '--help sourmashsketch' : 'Show sourmash `sketch` CLI options',
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422 '--help sourmashgather' : 'Show sourmash `gather` CLI options',
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423 '--help sourmashsearch' : 'Show sourmash `search` CLI options',
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424 '--help sfhpy' : 'Show sourmash_filter_hits.py CLI options',
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425 '--help flye' : 'Show flye CLI options',
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426 '--help mlst' : 'Show mlst CLI options',
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427 '--help abricate' : 'Show abricate CLI options',
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428 '--help gsrpy' : 'Show gen_salmon_res_table.py CLI options\n'
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429 ]
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430
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431 if (params.help.getClass().toString() =~ /Boolean/ || uHelp.size() == 0) {
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432 println conciseHelp('fastp,mash')
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433 helptext.putAll(defaultHelp)
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434 } else {
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435 params.help.tokenize(',').each { h ->
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436 if (defaultHelp.keySet().findAll{ it =~ /(?i)\b${h}\b/ }.size() == 0) {
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437 println conciseHelp('fastp,mash')
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438 stopNow("Tool [ ${h} ] is not a part of ${params.pipeline} pipeline.")
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439 }
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440 }
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441
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442 helptext.putAll(
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443 fastqEntryPointHelp() +
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444 (uHelp =~ /(?i)\bfiltlong/ ? filtlongHelp(params).text : nH) +
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445 (uHelp =~ /(?i)\bmash/ ? mashscreenHelp(params).text : nH) +
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446 (uHelp =~ /(?i)\btuspy/ ? tuspyHelp(params).text : nH) +
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447 (uHelp =~ /(?i)\bsourmashsketch/ ? sourmashsketchHelp(params).text : nH) +
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448 (uHelp =~ /(?i)\bsourmashgather/ ? sourmashgatherHelp(params).text : nH) +
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449 (uHelp =~ /(?i)\bsourmashsearch/ ? sourmashsearchHelp(params).text : nH) +
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450 (uHelp =~ /(?i)\bsfhpy/ ? sfhpyHelp(params).text : nH) +
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451 (uHelp =~ /(?i)\bflye/ ? flyeHelp(params).text : nH) +
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452 (uHelp =~ /(?i)\bmlst/ ? mlstHelp(params).text : nH) +
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453 (uHelp =~ /(?i)\babricate/ ? abricateHelp(params).text : nH) +
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454 (uHelp =~ /(?i)\bgsrpy/ ? gsrpyHelp(params).text : nH) +
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455 wrapUpHelp()
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|
456 )
|
|
|
457 }
|
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458
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459 return addPadding(helptext)
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|
|
460 } |
