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1 // Screening and SNP Pipeline processing
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2 output_directory = file(params.output_directory)
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3 log_directory = file(params.log_directory)
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4 screen_log_dir = file(params.screen_log_dir)
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5 snp_log_dir = file(params.snp_log_dir)
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6 snp_directory = file(params.snp_directory)
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7
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8 if(params.tmp_dir == ""){
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9 temp_dir = ""
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10 } else{
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11 temp_dir = file(params.temp_dir)
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12 }
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13 ref_id_file = file(params.ref_id_file)
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14
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15 ref_mode = params.ref_mode
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16
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17 // Assess whether to rescue edge-filtered SNPs
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18 edge_rescue = "${params.rescue}" == "norescue" ? "norescue" : "rescue"
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19
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20 // Set paths for output files
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21 all_snpdiffs_list = file("${log_directory}/All_SNPDiffs.txt")
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22 snp_dirs_list = file("${log_directory}/SNP_Dirs.txt")
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23 screening_results_file = file("${output_directory}/Screening_Results.tsv")
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24 isolate_data_file = file("${output_directory}/Isolate_Data.tsv")
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25 snpdiffs_summary_file = file("${output_directory}/Raw_MUMmer_Summary.tsv")
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26
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27 // Get QC thresholds
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28 min_cov = params.min_cov.toFloat()
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29 min_length = params.min_len.toInteger()
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30 min_iden = params.min_iden.toFloat()
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31 reference_edge = params.ref_edge.toInteger()
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32 query_edge = params.query_edge.toInteger()
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33 max_missing = params.max_missing.toFloat()
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34 n_ref = params.n_ref.toInteger()
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35
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36 workflow {
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37 main:
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38 // Run SNP pipeline
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39 runSNPPipeline(query_data: all_snpdiffs, reference_data: ref_id_file)
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40 }
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41
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42 workflow runScreen {
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43
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44 take:
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45 all_snpdiffs
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46
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47 main:
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48
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49 all_snpdiffs
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50 .unique{it -> it[2]}
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51 .collect()
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52 | screenSNPDiffs
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53 }
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54
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55 process screenSNPDiffs{
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56
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57 input:
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58 val(all_snpdiffs)
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59
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60 script:
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61
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62 screenDiffs = file("${projectDir}/bin/screenSNPDiffs.py")
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63 """
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64 $params.load_python_module
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65 $params.load_bedtools_module
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66 python $screenDiffs --snpdiffs_file "${all_snpdiffs_list}" --log_dir "${screen_log_dir}" --min_cov "${min_cov}" --min_len "${min_length}" --min_iden "${min_iden}" --ref_edge "${reference_edge}" --query_edge "${query_edge}" --density_windows "${params.dwin}" --max_snps "${params.wsnps}" --trim_name "${params.trim_name}" --output_file "${screening_results_file}" --ref_id "${ref_id_file}" --tmp_dir "${temp_dir}"
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67 """
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68 }
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69
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70 workflow runSNPPipeline{
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71 take:
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72 all_snpdiffs
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73 reference_data
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74
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75 main:
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76
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77 query_snpdiffs = all_snpdiffs.map{tuple(it[0],it[2])}
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78 ref_snpdiffs = all_snpdiffs.map{tuple(it[1],it[2])}
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79
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80 stacked_snpdiffs = query_snpdiffs.concat(ref_snpdiffs)
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81 .collect().flatten().collate(2)
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82
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83 snp_dirs = stacked_snpdiffs
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84 .combine(reference_data)
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85 .filter{it -> it[0].toString() == it[2].toString()}
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86 .map{it -> tuple(it[0],it[1])}
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87 .groupTuple(by:0)
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88 .map { ref, diff_files -> tuple( ref.toString(), diff_files.collect() ) }
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89 | runSnpPipeline
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90
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91 //snp_dirs.collect() | compileResults
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92 }
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93
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94 process compileResults{
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95
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96 executor = 'local'
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97 cpus = 1
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98 maxForks = 1
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99
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100 input:
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101 val(snp_directories)
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102
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103 script:
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104
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105 compile_script = file("${projectDir}/bin/compileSNPResults.py")
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106 snp_dirs_list.write(snp_directories.join("\n")+ "\n")
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107 """
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108 $params.load_python_module
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109 python $compile_script --snp_dirs_file "${snp_dirs_list}" --output_directory "${snp_directory}" --isolate_data_file "${isolate_data_file}" --mummer_data_file "${snpdiffs_summary_file}"
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110 """
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111 }
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112
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113 process runSnpPipeline{
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114
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115 input:
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116 tuple val(reference_id),val(diff_files)
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117
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118 output:
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119 stdout
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120
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121 script:
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122
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123 snp_script = file("${projectDir}/bin/runSNPPipeline.py")
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124
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125 // Set + create output directory
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126 snp_dir = file("${snp_directory}/${reference_id}")
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127 snp_dir.mkdirs()
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128
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129 // Write SNPDiffs list
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130 out_snpdiffs = file("${snp_dir}/SNPDiffs.txt")
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131 out_snpdiffs.write(diff_files.join("\n")+ "\n")
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132 """
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133 $params.load_python_module
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134 $params.load_bedtools_module
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135 python $snp_script --reference_id "${reference_id}" --output_directory "${snp_dir}" --snpdiffs_file "${out_snpdiffs}" --log_directory "${snp_log_dir}" --min_cov "${min_cov}" --min_len "${min_length}" --min_iden "${min_iden}" --ref_edge "${reference_edge}" --query_edge "${query_edge}" --density_windows "${params.dwin}" --max_snps "${params.wsnps}" --trim_name "${params.trim_name}" --max_missing "${max_missing}" --tmp_dir "${temp_dir}" --rescue "${edge_rescue}"
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136 echo -n $snp_dir
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137 """
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138 } |
