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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 KRAKEN2_CLASSIFY
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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 `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
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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 or FASTA assembly of type `path` (`reads`) 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 [ id: 'FAL00870',
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27 strandedness: 'unstranded',
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28 single_end: true,
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29 is_assembly: false,
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30 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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31 kraken2_db: '/hpc/db/kraken2/standard-210914',
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32 ],
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33 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
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34 ]
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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 #### `meta`
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41
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42 Type: Groovy Map
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43
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44 A Groovy Map containing the metadata about the FASTQ / FASTA file.
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45
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46 Ex:
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47
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48 ```groovy
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49 [
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50 id: 'FAL00870',
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51 strandedness: 'unstranded',
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52 single_end: true,
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53 is_assembly: false,
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54 kraken2_db: '/hpc/db/kraken2/standard-210914'
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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 FASTQ files on which `kraken2` classification 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 ### `output:`
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71
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72 ___
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73
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74 Type: `tuple`
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75
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76 Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
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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 #### `kraken_report`
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82
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83 Type: `path`
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84
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85 NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
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86
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87 \
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88
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89
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90 #### `kraken_output`
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91
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92 Type: `path`
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93
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94 NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
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95
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96 \
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97
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98
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99 #### `classified`
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100
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101 Type: `path`
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102
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103 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`).
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104
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105 \
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106
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107
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108 #### `unclassified`
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109
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110 Type: `path`
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111
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112 NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
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113
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114 \
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115
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116
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117 #### `versions`
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118
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119 Type: `path`
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120
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121 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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