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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_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 FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from.
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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 a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) 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 kraken2_db: '/hpc/db/kraken2/standard-210914'
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30 ],
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31 '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt',
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32 '/hpc/scratch/test/FAL000870/f1.assembly.fasta'
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33 ]
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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 #### `meta`
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40
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41 Type: Groovy Map
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42
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43 A Groovy Map containing the metadata about the FASTA file.
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44
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45 Ex:
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46
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47 ```groovy
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48 [
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49 id: 'FAL00870',
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50 strandedness: 'unstranded',
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51 single_end: true,
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52 kraken2_db: '/hpc/db/kraken2/standard-210914'
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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
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58
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59 #### `kraken2_output`
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60
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61 Type: `path`
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62
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63 NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool.
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64
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65 \
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66
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67
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68 #### `assembly`
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69
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70 Type: `path`
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71
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72 NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format.
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73
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74 \
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75
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76
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77 ### `output:`
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78
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79 ___
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80
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81 Type: `tuple`
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82
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83 Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
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84
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85 \
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86
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87
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88 #### `asm_filtered_contigs`
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89
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90 Type: `path`
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91
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92 NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa.
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93
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94 \
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95
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96
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97 #### `versions`
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98
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99 Type: `path`
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100
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101 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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