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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 ABRICATE_SUMMARY
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5 ```
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6
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7 ## Description
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8
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9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
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10
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11 \
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12
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13
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14 ### `input:`
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15
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16 ___
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17
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18 Type: `tuple`
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19
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20 Takes in the following tuple of `abricate` database names of type `val` (`abdbs`) and a list of `abricate` result table files for all databases of type `path` (`abfiles`).
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21
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22 Ex:
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23
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24 ```groovy
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25 [
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26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
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27 [ '/data/sample1/f.ncbi.ab.txt',
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28 '/data/sample1/f.megares.ab.txt',
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29 '/data/sample1/f.resfinder.ab.txt',
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30 '/data/sample1/f.argannot.ab.txt',
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31 '/data/sample1/f2.ncbi.ab.txt',
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32 '/data/sample1/f2.megares.ab.txt',
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33 '/data/sample1/f2.resfinder.ab.txt',
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34 '/data/sample1/f2.argannot.ab.txt'
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35 ]
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36 ]
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37 ```
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38
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39 \
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40
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41
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42 #### `abdbs`
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43
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44 Type: `val`
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45
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46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
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47
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48 Ex:
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49
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50 ```groovy
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51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
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52 ```
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53
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54 \
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55
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56
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57 #### `abfiles`
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58
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59 Type: `path`
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60
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61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
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62
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63 \
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64
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65
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66 ### `output:`
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67
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68 ___
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69
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70 #### `ncbi`
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71
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72 Type: `tuple`
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73 \
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74 Optional: `true`
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75
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76 Outputs a tuple of `abricate` database key (`abricate_ncbi`) and summary result file from `abricate summary` command of type `path` (`ncbi`). This database includes only core AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbi.absum.txt`
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77
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78 \
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79
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80
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81 #### `ncbiamrplus`
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82
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83 Type: `tuple`
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84 \
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85 Optional: `true`
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86
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87 Outputs a tuple of `abricate` database key (`abricate_ncbiamrplus`) and summary result file from `abricate summary` command of type `path` (`ncbiamrplus`). This database includes both core AMR genes and plus AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbiamrplus.absum.txt`
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88
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89 \
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90
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91
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92 #### `resfinder`
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93
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94 Type: `tuple`
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95 \
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96 Optional: `true`
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97
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98 Outputs a tuple of `abricate` database key (`abricate_resfinder`) and summary result file from `abricate summary` command of type `path` (`resfinder`). This tuple is emitted optionally only where there are output files with suffix `.resfinder.absum.txt`
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99
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100 \
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101
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102
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103 #### `megares`
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104
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105 Type: `tuple`
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106 \
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107 Optional: `true`
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108
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109 Outputs a tuple of `abricate` database key (`abricate_megares`) and summary result file from `abricate summary` command of type `path` (`megares`). This tuple is emitted optionally only where there are output files with suffix `.megares.absum.txt`
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110
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111 \
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112
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113
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114 #### `argannot`
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115
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116 Type: `tuple`
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117 \
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118 Optional: `true`
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119
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120 Outputs a tuple of `abricate` database key (`abricate_argannot`) and summary result file from `abricate summary` command of type `path` (`argannot`). This tuple is emitted optionally only where there are output files with suffix `.argannot.absum.txt`
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121
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122 \
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123
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124
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125 #### `ecoli_vf`
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126
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127 Type: `tuple`
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128 \
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129 Optional: `true`
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130
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131 Outputs an **optional** tuple of `abricate` database key (`abricate_ecoli_vf`) and summary result file from `abricate summary` command of type `path` (`ecoli_vf`). This tuple is emitted only when there are output files with suffix `.ecoli_vf.absum.txt` within the `work` folder.
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132
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133 \
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134
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135
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136 #### `versions`
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137
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138 Type: `path`
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139
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140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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