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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 BBTOOLS_BBMERGE
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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 `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection.
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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 [
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27 id: 'FAL00870',
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28 strandedness: 'unstranded',
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29 single_end: false
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30 ],
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31 [
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32 '/hpc/scratch/test/f1.R1.fq.gz',
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33 '/hpc/scratch/test/f1.R2.fq.gz'
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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 \
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39
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40
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41 #### `meta`
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42
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43 Type: Groovy Map
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44
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45 A Groovy Map containing the metadata about the FASTQ file.
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46
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47 Ex:
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48
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49 ```groovy
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50 [
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51 id: 'FAL00870',
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52 strandedness: 'unstranded',
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53 single_end: true
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54 ]
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55 ```
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56
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57 \
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58
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59
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60 #### `reads`
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61
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62 Type: `path`
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63
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64 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
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65
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66 \
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67
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68
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69 #### `args`
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70
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71 Type: Groovy String
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72
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73 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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74
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75 Ex:
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76
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77 ```groovy
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78 withName: 'BBTOOLS_BBMERGE' {
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79 ext.args = 'minprog=0.5'
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80 }
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81 ```
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82
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83 ### `output:`
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84
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85 ___
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86
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87 Type: `tuple`
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88
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89 Outputs a tuple of metadata (`meta` from `input:`) and merged gzipped FASTQ file.
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90
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91 \
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92
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93
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94 #### `fastq`
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95
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96 Type: `path`
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97
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98 NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`).
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99
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100 \
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101
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102
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103 #### `log`
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104
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105 Type: `path`
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106
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107 NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`).
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108
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109 \
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110
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111
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112 #### `versions`
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113
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114 Type: `path`
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115
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116 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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