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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 AMRFINDERPLUS_RUN
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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 `amrfinder` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format per database.
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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 assemled contig FASTA file of input type `path` (`fasta`).
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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 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
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26 ```
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27
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28 \
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29
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30
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31 #### `meta`
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32
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33 Type: Groovy Map
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34
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35 A Groovy Map containing the metadata about the FASTQ file.
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36
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37 Ex:
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38
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39 ```groovy
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40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ]
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41 ```
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42
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43 \
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44
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45
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46 #### `fasta`
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47
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48 Type: `path`
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49
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50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
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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 #### `args`
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56
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57 Type: Groovy String
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58
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59 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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60
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61 Ex:
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62
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63 ```groovy
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64 withName: 'AMRFINDERPLUS_RUN' {
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65 ext.args = '--gpipe_org'
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66 }
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67 ```
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68
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69 ### `output:`
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70
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71 ___
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72
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73 Type: `tuple`
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74
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75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
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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 #### `report`
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81
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82 Type: `path`
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83
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84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
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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 #### `mutional_report`
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90
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91 Type: `path`
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92 \
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93 Optional: `true`
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94
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95 NextFlow output type of `path` pointing to the `amrfinder` mutation results table file (`.tsv`) per sample (`id:`). Obtaining this output will depend on the presence of the `organism` key in the metadata (`meta`). See example above.
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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 #### `versions`
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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 `.yml` file storing software versions for this process.
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