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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 = '0.5.0'
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5 db_mode = 'mitomine2'
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6 db_root = '/server/galaxy/tool-data/nowayout-db'
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7 nowo_thresholds = 'strict'
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8 fastp_run = true
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9 fastp_failed_out = false
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10 fastp_merged_out = false
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11 fastp_overlapped_out = false
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12 fastp_6 = false
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13 fastp_reads_to_process = 0
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14 fastp_fix_mgi_id = false
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15 fastp_A = false
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16 fastp_use_custom_adapters = false
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17 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
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18 + File.separator
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19 + 'assets'
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20 + File.separator
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21 + 'adaptors.fa' : false)
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22 fastp_f = 0
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23 fastp_t = 0
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24 fastp_b = 0
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25 fastp_F = 0
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26 fastp_T = 0
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27 fastp_B = 0
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28 fastp_dedup = true
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29 fastp_dup_calc_accuracy = 6
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30 fastp_poly_g_min_len = 10
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31 fastp_G = true
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32 fastp_x = false
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33 fastp_poly_x_min_len = 10
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34 fastp_cut_front = true
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35 fastp_cut_tail = false
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36 fastp_cut_right = true
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37 fastp_W = 20
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38 fastp_M = 30
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39 fastp_q = 30
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40 fastp_u = 40
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41 fastp_n = 5
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42 fastp_e = 0
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43 fastp_l = 35
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44 fastp_max_len = 0
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45 fastp_y = true
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46 fastp_Y = 30
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47 fastp_U = false
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48 fastp_umi_loc = false
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49 fastp_umi_len = false
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50 fastp_umi_prefix = false
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51 fastp_umi_skip = false
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52 fastp_p = true
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53 fastp_P = 20
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54 kmaalign_run = true
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55 kmaalign_idx = ("${params.db_root}"
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56 + File.separator
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57 + "kma"
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58 + File.separator
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59 + "${params.db_mode}")
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60 kmaalign_ignorequals = false
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61 kmaalign_int = false
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62 kmaalign_ef = false
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63 kmaalign_vcf = false
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64 kmaalign_sam = false
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65 kmaalign_nc = true
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66 kmaalign_na = true
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67 kmaalign_nf = false
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68 kmaalign_a = false
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69 kmaalign_and = true
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70 kmaalign_oa = false
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71 kmaalign_bc = false
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72 kmaalign_bcNano = false
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73 kmaalign_bcd = false
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74 kmaalign_bcg = false
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75 kmaalign_ID = (params.nowo_thresholds =~ /strict|mild/ ? 85.0 : 50.0)
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76 kmaalign_md = false
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77 kmaalign_dense = false
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78 kmaalign_ref_fsa = false
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79 kmaalign_Mt1 = false
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80 kmaalign_1t1 = false
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81 kmaalign_mrs = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
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82 kmaalign_mrc = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
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83 kmaalign_mp = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
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84 kmaalign_eq = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
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85 kmaalign_mrs = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrs)
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86 kmaalign_mrc = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrc)
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87 kmaalign_mp = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_mp)
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88 kmaalign_eq = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_eq)
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89 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
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90 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
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91 kmaalign_mq = false
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92 kmaalign_5p = false
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93 kmaalign_3p = false
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94 kmaalign_apm = false
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95 kmaalign_cge = false
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96 tuspy_gd = false
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97 seqkit_grep_run = true
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98 seqkit_grep_n = false
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99 seqkit_grep_s = false
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100 seqkit_grep_c = false
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101 seqkit_grep_C = false
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102 seqkit_grep_i = false
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103 seqkit_grep_v = false
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104 seqkit_grep_m = false
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105 seqkit_grep_r = false
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106 salmonidx_run = true
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107 salmonidx_k = false
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108 salmonidx_gencode = false
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109 salmonidx_features = false
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110 salmonidx_keepDuplicates = true
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111 salmonidx_keepFixedFasta = false
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112 salmonidx_filterSize = false
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113 salmonidx_sparse = false
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114 salmonidx_n = true
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115 salmonidx_decoys = false
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116 salmonalign_libtype = 'SF'
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117 ref_fna = ("${params.db_root}"
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118 + File.separator
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119 + "reference"
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120 + File.separator
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121 + "${params.db_mode}"
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122 + ".fna")
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123 sourmash_k = (params.nowo_thresholds ==~ /strict/ ? 71 : 51)
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124 sourmash_scale = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
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125 sourmashsketch_run = true
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126 sourmashsketch_mode = 'dna'
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127 sourmashsketch_file = false
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128 sourmashsketch_f = false
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129 sourmashsketch_name = false
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130 sourmashsketch_p = "'abund,scaled=${params.sourmash_scale},k=${params.sourmash_k}'"
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131 sourmashsketch_randomize = false
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132 sourmashgather_run = (params.sourmashsketch_run ?: false)
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133 sourmashgather_n = false
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134 sourmashgather_thr_bp = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
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135 sourmashgather_ignoreabn = false
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136 sourmashgather_prefetch = false
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137 sourmashgather_noprefetch = false
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138 sourmashgather_ani_ci = true
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139 sourmashgather_k = "${params.sourmash_k}"
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140 sourmashgather_protein = false
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141 sourmashgather_rna = false
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142 sourmashgather_nuc = false
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143 sourmashgather_noprotein = false
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144 sourmashgather_dayhoff = false
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145 sourmashgather_nodayhoff = false
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146 sourmashgather_hp = false
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147 sourmashgather_nohp = false
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148 sourmashgather_dna = true
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149 sourmashgather_nodna = false
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150 sourmashgather_scaled = false
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151 sourmashgather_inc_pat = false
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152 sourmashgather_exc_pat = false
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153 sfhpy_run = true
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154 sfhpy_fcn = 'f_match'
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155 sfhpy_fcv = (params.nowo_thresholds ==~ /strict/ ? "0.8" : "0.5")
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156 sfhpy_gt = true
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157 sfhpy_lt = false
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158 sfhpy_all = true
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159 lineages_csv = ("${params.db_root}"
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160 + File.separator
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161 + "taxonomy"
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162 + File.separator
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163 + "${params.db_mode}"
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164 + File.separator
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165 + "lineages.csv")
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166 gsalkronapy_run = true
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167 gsalkronapy_sf = 10000
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168 gsalkronapy_smres_suffix = false
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169 gsalkronapy_failed_suffix = false
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170 gsalkronapy_num_lin_cols = false
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171 gsalkronapy_lin_regex = false
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172 krona_ktIT_run = true
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173 krona_ktIT_n = 'all'
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174 krona_ktIT_q = false
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175 krona_ktIT_c = false
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176 krona_res_suffix = '.krona.tsv'
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177 fq_filter_by_len = 0
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178 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
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179 fq2_suffix = '_R2_001.fastq.gz'
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180 } |
