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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 KMA_ALIGN
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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 `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
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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 metadata (`meta`) and a list of reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder per sample (`id:`).
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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 [
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27 id: 'FAL00870',
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28 strandedness: 'unstranded',
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29 single_end: false
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30 ],
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31 [
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32 '/hpc/scratch/test/f1.R1.fq.gz',
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33 '/hpc/scratch/test/f1.R2.fq.gz'
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34 ],
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35 '/path/to/kma/index/folder'
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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 #### `meta`
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43
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44 Type: Groovy Map
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45
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46 A Groovy Map containing the metadata about the FASTQ file.
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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 [
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52 id: 'FAL00870',
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53 strandedness: 'unstranded',
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54 single_end: true
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55 ]
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56 ```
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57
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58 \
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59
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60
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61 #### `reads`
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62
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63 Type: `path`
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64
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65 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
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66
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67 \
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68
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69
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70 #### `index`
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71
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72 Type: `path`
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73
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74 NextFlow input type of `path` pointing to folder containing `kma` index files.
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75
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76 \
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77
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78
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79 #### `args`
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80
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81 Type: Groovy String
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82
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83 String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
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84
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85 Ex:
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86
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87 ```groovy
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88 withName: 'KMA_ALIGN' {
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89 ext.args = '-mint2'
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90 }
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91 ```
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92
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93 ### `output:`
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94
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95 ___
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96
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97 Type: `tuple`
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98
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99 Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
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100
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101 \
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102
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103
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104 #### `res`
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105
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106 Type: `path`
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107
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108 NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
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109
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110 \
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111
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112
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113 #### `mapstat`
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114
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115 Type: `path`
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116
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117 NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
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118
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119 \
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120
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121
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122 #### `hits`
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123
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124 Type: `path`
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125
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126 NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
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127
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128 \
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129
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130
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131 #### `versions`
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132
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133 Type: `path`
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134
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135 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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