Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_iwdr.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 from pathlib import Path |
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2 from typing import Any |
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3 |
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4 from cwltool.main import main |
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5 |
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6 from .util import ( |
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7 get_data, |
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8 get_main_output, |
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9 get_windows_safe_factory, |
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10 needs_docker, |
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11 needs_singularity, |
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12 windows_needs_docker, |
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13 ) |
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14 |
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15 |
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16 @windows_needs_docker |
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17 def test_newline_in_entry() -> None: |
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18 """Files in a InitialWorkingDirectory are created with a newline character.""" |
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19 factory = get_windows_safe_factory() |
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20 echo = factory.make(get_data("tests/wf/iwdr-entry.cwl")) |
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21 assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"} |
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22 |
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23 |
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24 @needs_docker |
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25 def test_empty_file_creation() -> None: |
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26 """An empty file can be created in InitialWorkingDirectory.""" |
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27 err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")]) |
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28 assert err_code == 0 |
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29 |
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30 |
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31 @needs_docker |
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32 def test_directory_literal_with_real_inputs_inside(tmp_path: Path) -> None: |
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33 """Cope with unmoveable files in the output directory created by Docker+IWDR.""" |
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34 err_code, _, _ = get_main_output( |
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35 [ |
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36 "--out", |
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37 str(tmp_path), |
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38 get_data("tests/iwdr_dir_literal_real_file.cwl"), |
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39 "--example={}".format(get_data("tests/__init__.py")), |
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40 ] |
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41 ) |
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42 assert err_code == 0 |
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43 |
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44 |
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45 @needs_docker |
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46 def test_iwdr_permutations(tmp_path_factory: Any) -> None: |
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47 misc = tmp_path_factory.mktemp("misc") |
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48 fifth = str(tmp_path_factory.mktemp("fifth")) |
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49 sixth = str(tmp_path_factory.mktemp("sixth")) |
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50 seventh = str(tmp_path_factory.mktemp("seventh")) |
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51 eighth = str(tmp_path_factory.mktemp("eighth")) |
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52 first = misc / "first" |
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53 first.touch() |
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54 second = misc / "second" |
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55 second.touch() |
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56 third = misc / "third" |
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57 third.touch() |
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58 fourth = misc / "fourth" |
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59 fourth.touch() |
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60 outdir = str(tmp_path_factory.mktemp("outdir")) |
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61 assert ( |
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62 main( |
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63 [ |
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64 "--outdir", |
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65 outdir, |
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66 "--enable-dev", |
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67 get_data("tests/wf/iwdr_permutations.cwl"), |
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68 "--first", |
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69 str(first), |
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70 "--second", |
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71 str(second), |
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72 "--third", |
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73 str(third), |
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74 "--fourth", |
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75 str(fourth), |
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76 "--fifth", |
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77 fifth, |
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78 "--sixth", |
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79 sixth, |
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80 "--seventh", |
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81 seventh, |
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82 "--eighth", |
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83 eighth, |
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84 ] |
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85 ) |
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86 == 0 |
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87 ) |
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88 |
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89 |
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90 @needs_docker |
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91 def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None: |
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92 misc = tmp_path_factory.mktemp("misc") |
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93 fifth = str(tmp_path_factory.mktemp("fifth")) |
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94 sixth = str(tmp_path_factory.mktemp("sixth")) |
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95 seventh = str(tmp_path_factory.mktemp("seventh")) |
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96 eighth = str(tmp_path_factory.mktemp("eighth")) |
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97 first = misc / "first" |
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98 first.touch() |
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99 second = misc / "second" |
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100 second.touch() |
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101 third = misc / "third" |
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102 third.touch() |
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103 fourth = misc / "fourth" |
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104 fourth.touch() |
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105 outdir = str(tmp_path_factory.mktemp("outdir")) |
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106 assert ( |
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107 main( |
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108 [ |
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109 "--outdir", |
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110 outdir, |
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111 "--enable-ext", |
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112 "--enable-dev", |
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113 "--overrides", |
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114 get_data("tests/wf/iwdr_permutations_inplace.yml"), |
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115 get_data("tests/wf/iwdr_permutations.cwl"), |
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116 "--first", |
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117 str(first), |
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118 "--second", |
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119 str(second), |
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120 "--third", |
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121 str(third), |
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122 "--fourth", |
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123 str(fourth), |
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124 "--fifth", |
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125 fifth, |
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126 "--sixth", |
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127 sixth, |
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128 "--seventh", |
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129 seventh, |
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130 "--eighth", |
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131 eighth, |
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132 ] |
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133 ) |
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134 == 0 |
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135 ) |
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136 |
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137 |
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138 @needs_singularity |
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139 def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None: |
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140 misc = tmp_path_factory.mktemp("misc") |
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141 fifth = str(tmp_path_factory.mktemp("fifth")) |
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142 sixth = str(tmp_path_factory.mktemp("sixth")) |
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143 seventh = str(tmp_path_factory.mktemp("seventh")) |
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144 eighth = str(tmp_path_factory.mktemp("eighth")) |
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145 first = misc / "first" |
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146 first.touch() |
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147 second = misc / "second" |
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148 second.touch() |
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149 third = misc / "third" |
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150 third.touch() |
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151 fourth = misc / "fourth" |
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152 fourth.touch() |
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153 outdir = str(tmp_path_factory.mktemp("outdir")) |
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154 assert ( |
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155 main( |
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156 [ |
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157 "--outdir", |
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158 outdir, |
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159 "--enable-dev", |
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160 "--singularity", |
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161 get_data("tests/wf/iwdr_permutations.cwl"), |
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162 "--first", |
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163 str(first), |
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164 "--second", |
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165 str(second), |
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166 "--third", |
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167 str(third), |
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168 "--fourth", |
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169 str(fourth), |
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170 "--fifth", |
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171 fifth, |
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172 "--sixth", |
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173 sixth, |
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174 "--seventh", |
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175 seventh, |
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176 "--eighth", |
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177 eighth, |
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178 ] |
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179 ) |
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180 == 0 |
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181 ) |
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182 |
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183 |
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184 @needs_singularity |
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185 def test_iwdr_permutations_singularity_inplace(tmp_path_factory: Any) -> None: |
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186 misc = tmp_path_factory.mktemp("misc") |
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187 fifth = str(tmp_path_factory.mktemp("fifth")) |
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188 sixth = str(tmp_path_factory.mktemp("sixth")) |
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189 seventh = str(tmp_path_factory.mktemp("seventh")) |
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190 eighth = str(tmp_path_factory.mktemp("eighth")) |
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191 first = misc / "first" |
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192 first.touch() |
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193 second = misc / "second" |
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194 second.touch() |
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195 third = misc / "third" |
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196 third.touch() |
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197 fourth = misc / "fourth" |
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198 fourth.touch() |
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199 outdir = str(tmp_path_factory.mktemp("outdir")) |
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200 assert ( |
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201 main( |
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202 [ |
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203 "--outdir", |
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204 outdir, |
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205 "--singularity", |
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206 "--enable-ext", |
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207 "--enable-dev", |
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208 "--overrides", |
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209 get_data("tests/wf/iwdr_permutations_inplace.yml"), |
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210 get_data("tests/wf/iwdr_permutations.cwl"), |
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211 "--first", |
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212 str(first), |
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213 "--second", |
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214 str(second), |
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215 "--third", |
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216 str(third), |
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217 "--fourth", |
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218 str(fourth), |
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219 "--fifth", |
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220 fifth, |
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221 "--sixth", |
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222 sixth, |
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223 "--seventh", |
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224 seventh, |
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225 "--eighth", |
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226 eighth, |
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227 ] |
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228 ) |
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229 == 0 |
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230 ) |