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1 # NextFlow DSL2 Module
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2
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3 ```bash
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4 CENTRIFUGE_CLASSIFY
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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 `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output 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 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 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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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
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58 #### `reads`
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59
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60 Type: `path`
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61
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62 NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run.
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63
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64 \
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65
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66
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67 #### `args`
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68
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69 Type: Groovy String
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70
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71 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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72
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73 Ex:
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74
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75 ```groovy
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76 withName: 'CENTRIFUGE_CLASSIFY' {
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77 ext.args = '--met 3'
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78 }
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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
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84 ### `output:`
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85
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86 ___
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87
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88 Type: `tuple`
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89
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90 Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
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91
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92 \
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93
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94
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95 #### `report`
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96
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97 Type: `path`
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98
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99 NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
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100
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101 \
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102
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103
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104 #### `output`
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105
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106 Type: `path`
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107
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108 NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
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109
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110 \
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111
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112
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113 #### `kreport`
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114
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115 Type: `path`
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116
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117 NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
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118
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119 \
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120
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121
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122 #### `sam`
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123
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124 Type: `path`
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125 \
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126 Optional: `true`
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127
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128 NextFlow output type of `path` pointing to the `centrifuge` alignment results in SAM (`.sam`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_out_fmt_sam` command-line option when the NextFlow pipeline is called.
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129
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130 \
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131
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132
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133 #### `fastq_mapped`
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134
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135 Type: `path`
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136 \
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137 Optional: `true`
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138
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139 NextFlow output type of `path` pointing to the `centrifuge` alignment results in FASTQ (`.fastq.gz`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_aligned` command-line option when the NextFlow pipeline is called.
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140
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141 \
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142
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143
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144 #### `fastq_unmapped`
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145
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146 Type: `path`
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147 \
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148 Optional: `true`
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149
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150 NextFlow output type of `path` pointing to the `centrifuge` FASTQ (`.fastq.gz`) files of unaligned reads per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_unaligned` command-line option when the NextFlow pipeline is called.
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151
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152 \
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153
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154
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155 #### `versions`
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156
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157 Type: `path`
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158
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159 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
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