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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 SEQSERO2
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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 `seqsero2` tool on a list of assembled *Salmonella* contigs in FASTA format or sequencing reads in FASTQ 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 assemled contig FASTA files or list of sequencing reads in FASTQ format of input type `path` (`reads_or_asm`).
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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 files or assembly FASTA files.
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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 ]
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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 #### `reads_or_asm`
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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 or sequencing reads in FASTQ 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: 'SEQSERO2' {
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65 ext.args = '-b mem'
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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
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72 ### `output:`
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73
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74 ___
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75
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76 Type: `tuple`
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77
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78 Outputs a tuple of metadata (`meta` from `input:`) and list of `seqsero2` result files (`serotyped`).
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79
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80 \
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81
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82
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83 #### `serotyped`
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84
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85 Type: `path`
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86
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87 NextFlow output type of `path` pointing to the `seqsero2` results table file per sample (`id:`).
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88
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89 \
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90
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91
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92 #### `versions`
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93
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94 Type: `path`
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95
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96 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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