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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 SEQKIT_GREP
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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 `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input 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` (`reads`) 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 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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30 ],
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31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
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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 strandedness: 'unstranded',
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50 single_end: true
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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
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56
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57 #### `reads`
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58
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59 Type: `path`
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60
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61 NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run.
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62
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63 \
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64
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65
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66 #### `pattern_file`
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67
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68 Type: path
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69
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70 NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted.
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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 #### `args`
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76
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77 Type: Groovy String
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78
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79 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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80
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81 Ex:
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82
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83 ```groovy
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84 withName: 'SEQKIT_GREP' {
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85 ext.args = '--only-positive-strand'
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86 }
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87 ```
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88
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89 ### `output:`
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90
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91 ___
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92
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93 Type: `tuple`
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94
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95 Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
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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 #### `fastx`
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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 FASTQ format filtered gzipped file per sample (`id:`).
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105
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106 \
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107
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108
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109 #### `versions`
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110
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111 Type: `path`
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112
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113 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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