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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 MASH_SCREEN
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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 `mash screen` on the input FASTQ file.
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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` (`query`) 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 ],
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29 [
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30 '/hpc/scratch/test/f1.fq.gz'
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31 ]
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32 ]
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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 #### `meta`
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39
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40 Type: Groovy Map
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41
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42 A Groovy Map containing the metadata about the FASTQ file.
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43
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44 Ex:
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45
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46 ```groovy
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47 [
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48 id: 'FAL00870'
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49 ]
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50 ```
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51
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52 \
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53
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54
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55 #### `query`
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56
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57 Type: `path`
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58
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59 NextFlow input type of `path` pointing to FASTQ file to be screened.
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60
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61 \
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62
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63
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64 ### `output:`
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65
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66 ___
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67
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68 Type: `tuple`
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69
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70 Outputs a tuple of metadata (`meta` from `input:`) and `mash screen` result file ending with suffix `.screened`.
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71
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72 \
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73
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74
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75 #### `screened`
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76
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77 Type: `path`
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78
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79 NextFlow output type of `path` pointing to the result (`*.screened`) of the `mash screen` command per sample (`id:`).
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80
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81 \
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82
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83
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84 #### `versions`
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85
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86 Type: `path`
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87
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88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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