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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 SALMON_QUANT
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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 `salmon quant` in `reads` or `alignments` mode. The inputs can be either the alignment (Ex: `.bam`) files or read (Ex: `.fastq.gz`) files.
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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 either an alignment file or reads file and a `salmon index` or a transcript FASTA file 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: true
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30 ],
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31 [
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32 '/hpc/scratch/test/FAL00870_R1.fastq.gz'
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33 ],
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34 [
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35 '/hpc/scratch/test/salmon_idx_for_FAL00870'
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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
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42
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43 #### `meta`
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44
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45 Type: Groovy Map
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46
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47 A Groovy Map containing the metadata about the input setup for `salmon quant`.
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48
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49 Ex:
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50
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51 ```groovy
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52 [
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53 id: 'FAL00870',
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54 strandedness: 'unstranded',
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55 single_end: true
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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
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61
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62 #### `reads_or_bam`
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63
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64 Type: `path`
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65
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66 NextFlow input type of `path` pointing to either an alignment file (Ex: `.bam`) or a reads file (Ex: `.fastq.gz`) on which `salmon quant` should be run.
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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 #### `index_or_tr_fasta`
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72
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73 Type: `path`
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74
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75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
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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 #### `args`
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81
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82 Type: Groovy String
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83
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84 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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85
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86 Ex:
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87
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88 ```groovy
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89 withName: 'SALMON_QUANT' {
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90 ext.args = '--vbPrior 0.02'
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91 }
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92 ```
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93
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94 ### `output:`
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95
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96 ___
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97
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98 Type: `tuple`
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99
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100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
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101
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102 \
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103
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104
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105 #### `results`
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106
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107 Type: `path`
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108
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109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
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110
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111 \
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112
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113
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114 #### `versions`
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115
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116 Type: `path`
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117
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118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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