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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 CENTRIFUGE_EXTRACT
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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 Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids.
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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 2 tuples:
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21
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22 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`).
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23
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24 - A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`).
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25
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26 Ex:
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27
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28 ```groovy
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29 [
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30 [ id: 'FAL00870',
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31 strandedness: 'unstranded',
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32 single_end: true,
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33 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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34 ],
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35 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt'
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36 ]
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37
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38 [
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39 [ id: 'FAL00870',
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40 strandedness: 'unstranded',
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41 single_end: true,
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42 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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43 ],
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44 '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt'
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45 ]
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46 ```
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47
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48 \
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49
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50
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51 #### `meta`
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52
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53 Type: Groovy Map
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54
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55 A Groovy Map containing the metadata about the FASTQ file.
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56
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57 Ex:
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58
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59 ```groovy
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60 [
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61 id: 'FAL00870',
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62 strandedness: 'unstranded',
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63 single_end: true,
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64 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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65 ]
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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
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71 #### `centrifuge_report`
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72
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73 Type: `path`
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74
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75 NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool.
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76
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77 \
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78
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79
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80 #### `centrifuge_output`
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81
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82 Type: `path`
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83
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84 NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool.
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85
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86 \
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87
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88
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89 ### `output:`
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90
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91 ___
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92
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93 Type: `tuple`
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94
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95 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
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96
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97 \
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98
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99
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100 #### `extracted`
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101
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102 Type: `path`
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103
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104 NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`).
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105
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106 \
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107
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108
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109 #### `versions`
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110
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111 Type: `path`
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112
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113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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