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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 MEGAHIT_ASSEMBLE
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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 `megahit` assembler tool on a list of read files 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 FASTQ files (short reads) of input type `path` (`reads`).
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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_merged.fq.gz' ]
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26 [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ]
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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
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32 #### `meta`
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33
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34 Type: Groovy Map
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35
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36 A Groovy Map containing the metadata about the FASTQ file.
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37
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38 Ex:
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39
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40 ```groovy
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41 [ id: 'KB01', strandedness: 'unstranded', single_end: true ]
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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
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47 #### `reads`
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48
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49 Type: `path`
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50
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51 NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled.
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52
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53 \
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54
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55
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56 #### `args`
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57
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58 Type: Groovy String
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59
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60 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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61
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62 Ex:
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63
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64 ```groovy
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65 withName: 'MEGAHIT_ASSEMBLE' {
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66 ext.args = '--keep-tmp-files'
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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
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73 ### `output:`
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74
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75 ___
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76
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77 Type: `tuple`
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78
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79 Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format.
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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 #### `assembly`
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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 `megahit` assembler results file (`final.contigs.fa`) per sample (`id:`) i.e., the final assembled contigs file in FASTA format.
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89
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90 \
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91
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92
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93 #### `versions`
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94
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95 Type: `path`
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96
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97 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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