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1 params {
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2 workflow_conceived_by = 'Kranti Konganti'
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3 workflow_built_by = 'Kranti Konganti'
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4 workflow_version = '1.0.0'
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5 bcs_root_dbdir = '/tool/tool-data/cfsan_bettercallsal_db/latest'
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6 bcs_db_mode = 'snp'
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7 bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
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8 bcs_thresholds = 'strict'
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9 filtlong_run = true
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10 filtlong_keep_perc = false
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11 filtlong_target_bases = false
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12 filtlong_min_length = 1000
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13 filtlong_max_length = 20000
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14 filtlong_min_mean_q = 75
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15 filtlong_min_window_q = 75
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16 filtlong_a = false
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17 filtlong_1 = false
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18 filtlong_2 = false
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19 filtlong_len_weight = false
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20 filtlong_mean_q_weight = 30
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21 filtlong_window_q_weight = 30
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22 filtlong_trim = false
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23 filtlong_split = false
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24 filtlong_window_size = 250
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25 mashscreen_run = true
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26 mash_sketch = (params.bcs_root_dbdir
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27 + File.separator
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28 + 'mash_sketch'
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29 + File.separator
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30 + 'msh.k21.1000h.'
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31 + params.bcs_db_mode
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32 + '.msh')
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33 mashscreen_w = false
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34 mashscreen_i = false
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35 mashscreen_v = false
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36 tuspy_run = true
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37 tuspy_s = false
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38 tuspy_m = false
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39 tuspy_ps = (params.bcs_root_dbdir
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40 + File.separator
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41 + 'index_metadata'
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42 + File.separator
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43 + 'per_'
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44 + params.bcs_db_mode
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45 + params.bcs_db_mode_index
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46 + '.ACC2SERO.pickle')
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47 tuspy_gd = (params.bcs_root_dbdir
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48 + File.separator
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49 + 'scaffold_genomes')
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50 tuspy_gds = '_scaffolded_genomic.fna.gz'
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51 tuspy_n = 10
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52 tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
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53 sourmashsketch_run = true
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54 sourmashsketch_mode = 'dna'
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55 sourmashsketch_file = false
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56 sourmashsketch_f = false
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57 sourmashsketch_merge = false
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58 sourmashsketch_name = false
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59 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71,k=81,k=91,k=101'
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60 sourmashsketch_singleton = true
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61 sourmashsketch_randomize = false
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62 sourmashgather_run = (params.sourmashsketch_run ?: false)
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63 sourmashgather_n = false
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64 sourmashgather_thr_bp = false
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65 sourmashgather_ignoreabn = false
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66 sourmashgather_prefetch = false
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67 sourmashgather_noprefetch = false
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68 sourmashgather_ani_ci = true
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69 sourmashgather_k = 81
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70 sourmashgather_protein = false
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71 sourmashgather_noprotein = false
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72 sourmashgather_dayhoff = false
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73 sourmashgather_nodayhoff = false
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74 sourmashgather_hp = false
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75 sourmashgather_nohp = false
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76 sourmashgather_dna = true
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77 sourmashgather_nodna = false
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78 sourmashgather_scaled = false
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79 sourmashgather_inc_pat = false
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80 sourmashgather_exc_pat = false
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81 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
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82 sourmashsearch_n = false
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83 sourmashsearch_thr = '0'
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84 sourmashsearch_contain = false
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85 sourmashsearch_maxcontain = true
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86 sourmashsearch_ignoreabn = true
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87 sourmashsearch_ani_ci = false
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88 sourmashsearch_k = 81
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89 sourmashsearch_protein = false
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90 sourmashsearch_noprotein = false
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91 sourmashsearch_dayhoff = false
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92 sourmashsearch_nodayhoff = false
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93 sourmashsearch_hp = false
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94 sourmashsearch_nohp = false
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95 sourmashsearch_dna = true
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96 sourmashsearch_nodna = false
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97 sourmashsearch_scaled = false
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98 sourmashsearch_inc_pat = false
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99 sourmashsearch_exc_pat = false
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100 sfhpy_run = true
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101 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
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102 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.05)
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103 sfhpy_gt = true
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104 sfhpy_lt = false
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105 salmonalign_libtype = 'U'
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106 flye_run = true
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107 flye_pacbio_raw = false
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108 flye_pacbio_corr = false
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109 flye_pacbio_hifi = false
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110 flye_nano_raw = false
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111 flye_nano_corr = true
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112 flye_nano_hq = false
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113 flye_genome_size = false
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114 flye_polish_iter = '3'
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115 flye_min_overlap = false
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116 flye_scaffold = false
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117 flye_meta = true
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118 mm2_align_bam = true
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119 mm2_align_bam_sorted = false
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120 mm2_align_cigar_paf = false
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121 mm2_align_cigar_bam = false
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122 mlst_run = true
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123 mlst_scheme = 'senterica_achtman_2'
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124 mlst_legacy = true
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125 mlst_minid = 95
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126 mlst_mincov = 10
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127 mlst_minscore = 50
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128 abricate_run = true
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129 abricate_datadir = ("${projectDir}"
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130 + File.separator
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131 + 'assets'
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132 + File.separator
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133 + 'abricate_dbs')
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134 abricate_minid = 90
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135 abricate_mincov = 80
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136 abricate_summary_run = true
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137 gsrpy_run = true
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138 gsrpy_url = true
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139 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
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140 + File.separator
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141 + 'download_pdg_metadata'
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142 + File.separator
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143 + getPDGRelease(params.bcs_root_dbdir)
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144 + File.separator
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145 + getPDGRelease(params.bcs_root_dbdir)
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146 + '.reference_target.cluster_list.tsv')
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147 sourmashcompare_mode = 'ani,containment'
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148 fq_filter_by_len = 0
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149 fq_filename_delim_idx = 3
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150 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
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151 fq2_suffix = '_R2_001.fastq.gz'
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152 multiqc_run = true
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153 }
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154
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155 /*
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156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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157 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
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158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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159 */
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160
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161 def getPDGRelease(db_path) {
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162 db_path_obj = new File( db_path )
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163 def pdg_release = []
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164
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165 db_path_obj.eachDirRecurse {
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166 it.toString() =~ /PDG/ \
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167 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
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168 : null
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169 }
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170
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171 return pdg_release.unique().join('').toString()
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172 }
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