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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 CENTRIFUGE_CLASSIFY
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 9 Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
kkonganti@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `tuple`
kkonganti@105 19
kkonganti@105 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [
kkonganti@105 26 [ id: 'FAL00870',
kkonganti@105 27 strandedness: 'unstranded',
kkonganti@105 28 single_end: true,
kkonganti@105 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 30 ],
kkonganti@105 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@105 32 ]
kkonganti@105 33 ```
kkonganti@105 34
kkonganti@105 35 \
kkonganti@105 36  
kkonganti@105 37
kkonganti@105 38 #### `meta`
kkonganti@105 39
kkonganti@105 40 Type: Groovy Map
kkonganti@105 41
kkonganti@105 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105 43
kkonganti@105 44 Ex:
kkonganti@105 45
kkonganti@105 46 ```groovy
kkonganti@105 47 [
kkonganti@105 48 id: 'FAL00870',
kkonganti@105 49 strandedness: 'unstranded',
kkonganti@105 50 single_end: true,
kkonganti@105 51 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105 52 ]
kkonganti@105 53 ```
kkonganti@105 54
kkonganti@105 55 \
kkonganti@105 56  
kkonganti@105 57
kkonganti@105 58 #### `reads`
kkonganti@105 59
kkonganti@105 60 Type: `path`
kkonganti@105 61
kkonganti@105 62 NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run.
kkonganti@105 63
kkonganti@105 64 \
kkonganti@105 65  
kkonganti@105 66
kkonganti@105 67 #### `args`
kkonganti@105 68
kkonganti@105 69 Type: Groovy String
kkonganti@105 70
kkonganti@105 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.
kkonganti@105 72
kkonganti@105 73 Ex:
kkonganti@105 74
kkonganti@105 75 ```groovy
kkonganti@105 76 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@105 77 ext.args = '--met 3'
kkonganti@105 78 }
kkonganti@105 79 ```
kkonganti@105 80
kkonganti@105 81 \
kkonganti@105 82  
kkonganti@105 83
kkonganti@105 84 ### `output:`
kkonganti@105 85
kkonganti@105 86 ___
kkonganti@105 87
kkonganti@105 88 Type: `tuple`
kkonganti@105 89
kkonganti@105 90 Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
kkonganti@105 91
kkonganti@105 92 \
kkonganti@105 93  
kkonganti@105 94
kkonganti@105 95 #### `report`
kkonganti@105 96
kkonganti@105 97 Type: `path`
kkonganti@105 98
kkonganti@105 99 NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
kkonganti@105 100
kkonganti@105 101 \
kkonganti@105 102  
kkonganti@105 103
kkonganti@105 104 #### `output`
kkonganti@105 105
kkonganti@105 106 Type: `path`
kkonganti@105 107
kkonganti@105 108 NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
kkonganti@105 109
kkonganti@105 110 \
kkonganti@105 111  
kkonganti@105 112
kkonganti@105 113 #### `kreport`
kkonganti@105 114
kkonganti@105 115 Type: `path`
kkonganti@105 116
kkonganti@105 117 NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
kkonganti@105 118
kkonganti@105 119 \
kkonganti@105 120  
kkonganti@105 121
kkonganti@105 122 #### `sam`
kkonganti@105 123
kkonganti@105 124 Type: `path`
kkonganti@105 125 \
kkonganti@105 126 Optional: `true`
kkonganti@105 127
kkonganti@105 128 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.
kkonganti@105 129
kkonganti@105 130 \
kkonganti@105 131  
kkonganti@105 132
kkonganti@105 133 #### `fastq_mapped`
kkonganti@105 134
kkonganti@105 135 Type: `path`
kkonganti@105 136 \
kkonganti@105 137 Optional: `true`
kkonganti@105 138
kkonganti@105 139 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.
kkonganti@105 140
kkonganti@105 141 \
kkonganti@105 142  
kkonganti@105 143
kkonganti@105 144 #### `fastq_unmapped`
kkonganti@105 145
kkonganti@105 146 Type: `path`
kkonganti@105 147 \
kkonganti@105 148 Optional: `true`
kkonganti@105 149
kkonganti@105 150 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.
kkonganti@105 151
kkonganti@105 152 \
kkonganti@105 153  
kkonganti@105 154
kkonganti@105 155 #### `versions`
kkonganti@105 156
kkonganti@105 157 Type: `path`
kkonganti@105 158
kkonganti@105 159 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.