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1 // Include any necessary methods and modules
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2 include { stopNow; validateParamsForFASTQ } from "${params.routines}"
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3 include { GEN_SAMPLESHEET } from "${params.modules}${params.fs}gen_samplesheet${params.fs}main"
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4 include { SAMPLESHEET_CHECK } from "${params.modules}${params.fs}samplesheet_check${params.fs}main"
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5 include { CAT_FASTQ } from "${params.modules}${params.fs}cat${params.fs}fastq${params.fs}main"
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6 include { SEQKIT_SEQ } from "${params.modules}${params.fs}seqkit${params.fs}seq${params.fs}main"
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7
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8 // Validate 4 required workflow parameters if
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9 // FASTQ files are the input for the
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10 // entry point.
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11 validateParamsForFASTQ()
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12
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13 // Start the subworkflow
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14 workflow PROCESS_FASTQ {
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15 main:
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16 versions = Channel.empty()
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17 input_ch = Channel.empty()
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18 reads = Channel.empty()
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19
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20 def input = file( (params.input ?: params.metadata) )
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21
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22 if (params.input) {
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23 def fastq_files = []
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24
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25 if (params.fq_suffix == null) {
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26 stopNow("We need to know what suffix the FASTQ files ends with inside the\n" +
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27 "directory. Please use the --fq_suffix option to indicate the file\n" +
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28 "suffix by which the files are to be collected to run the pipeline on.")
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29 }
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30
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31 if (params.fq_strandedness == null) {
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32 stopNow("We need to know if the FASTQ files inside the directory\n" +
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33 "are sequenced using stranded or non-stranded sequencing. This is generally\n" +
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34 "required if the sequencing experiment is RNA-SEQ. For almost all of the other\n" +
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35 "cases, you can probably use the --fq_strandedness unstranded option to indicate\n" +
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36 "that the reads are unstranded.")
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37 }
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38
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39 if (params.fq_filename_delim == null || params.fq_filename_delim_idx == null) {
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40 stopNow("We need to know the delimiter of the filename of the FASTQ files.\n" +
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41 "By default the filename delimiter is _ (underscore). This delimiter character\n" +
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42 "is used to split and assign a group name. The group name can be controlled by\n" +
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43 "using the --fq_filename_delim_idx option (1-based). For example, if the FASTQ\n" +
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44 "filename is WT_REP1_001.fastq, then to create a group WT, use the following\n" +
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45 "options: --fq_filename_delim _ --fq_filename_delim_idx 1")
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46 }
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47
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48 if (!input.exists()) {
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49 stopNow("The input directory,\n${params.input}\ndoes not exist!")
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50 }
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51
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52 input.eachFileRecurse {
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53 it.name.endsWith("${params.fq_suffix}") ? fastq_files << it : fastq_files << null
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54 }
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55
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56 if (fastq_files.findAll{ it != null }.size() == 0) {
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57 stopNow("The input directory,\n${params.input}\nis empty! or does not " +
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58 "have FASTQ files ending with the suffix: ${params.fq_suffix}")
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59 }
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60
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61 GEN_SAMPLESHEET( Channel.fromPath(params.input, type: 'dir') )
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62 GEN_SAMPLESHEET.out.csv.set{ input_ch }
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63 versions.mix( GEN_SAMPLESHEET.out.versions )
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64 .set { versions }
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65 } else if (params.metadata) {
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66 if (!input.exists()) {
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67 stopNow("The metadata CSV file,\n${params.metadata}\ndoes not exist!")
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68 }
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69
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70 if (input.size() <= 0) {
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71 stopNow("The metadata CSV file,\n${params.metadata}\nis empty!")
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72 }
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73
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74 Channel.fromPath(params.metadata, type: 'file')
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75 .set { input_ch }
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76 }
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77
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78 SAMPLESHEET_CHECK( input_ch )
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79 .csv
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80 .splitCsv( header: true, sep: ',')
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81 .map { create_fastq_channel(it) }
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82 .groupTuple(by: [0])
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83 .branch {
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84 meta, fastq ->
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85 single : fastq.size() == 1
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86 return [ meta, fastq.flatten() ]
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87 multiple : fastq.size() > 1
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88 return [ meta, fastq.flatten() ]
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89 }
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90 .set { reads }
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91
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92 CAT_FASTQ( reads.multiple )
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93 .catted_reads
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94 .mix( reads.single )
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95 .set { processed_reads }
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96
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97 if (params.fq_filter_by_len.toInteger() > 0) {
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98 SEQKIT_SEQ( processed_reads )
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99 .fastx
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100 .set { processed_reads }
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101
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102 versions.mix( SEQKIT_SEQ.out.versions.first().ifEmpty(null) )
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103 .set { versions }
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104 }
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105
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106 versions.mix(
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107 SAMPLESHEET_CHECK.out.versions,
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108 CAT_FASTQ.out.versions.first().ifEmpty(null)
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109 )
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110 .set { versions }
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111
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112 emit:
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113 processed_reads
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114 versions
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115 }
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116
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117 // Function to get list of [ meta, [ fq1, fq2 ] ]
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118 def create_fastq_channel(LinkedHashMap row) {
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119
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120 def meta = [:]
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121 meta.id = row.sample
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122 meta.single_end = row.single_end.toBoolean()
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123 meta.strandedness = row.strandedness
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124 meta.id = meta.id.split(params.fq_filename_delim)[0..params.fq_filename_delim_idx.toInteger() - 1]
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125 .join(params.fq_filename_delim)
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126 meta.id = (meta.id =~ /\./ ? meta.id.take(meta.id.indexOf('.')) : meta.id)
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127
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128 def array = []
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129
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130 if (!file(row.fq1).exists()) {
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131 stopNow("Please check input metadata CSV. The following Read 1 FASTQ file does not exist!" +
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132 "\n${row.fq1}")
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133 }
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134 if (meta.single_end) {
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135 array = [ meta, [ file(row.fq1) ] ]
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136 } else {
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137 if (!file(row.fq2).exists()) {
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138 stopNow("Please check input metadata CSV. The following Read 2 FASTQ file does not exist!" +
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139 "\n${row.fq2}")
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140 }
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141 array = [ meta, [ file(row.fq1), file(row.fq2) ] ]
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142 }
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143 return array
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144 } |
