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author kkonganti
date Wed, 29 Jun 2022 15:27:50 -0400
parents 77494b0fa3c7
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kkonganti@0 1 # NextFlow DSL2 Module
kkonganti@0 2
kkonganti@0 3 ```bash
kkonganti@0 4 CENTRIFUGE_CLASSIFY
kkonganti@0 5 ```
kkonganti@0 6
kkonganti@0 7 ## Description
kkonganti@0 8
kkonganti@0 9 Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
kkonganti@0 10
kkonganti@0 11 \
kkonganti@0 12  
kkonganti@0 13
kkonganti@0 14 ### `input:`
kkonganti@0 15
kkonganti@0 16 ___
kkonganti@0 17
kkonganti@0 18 Type: `tuple`
kkonganti@0 19
kkonganti@0 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@0 21
kkonganti@0 22 Ex:
kkonganti@0 23
kkonganti@0 24 ```groovy
kkonganti@0 25 [
kkonganti@0 26 [ id: 'FAL00870',
kkonganti@0 27 strandedness: 'unstranded',
kkonganti@0 28 single_end: true,
kkonganti@0 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@0 30 ],
kkonganti@0 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@0 32 ]
kkonganti@0 33 ```
kkonganti@0 34
kkonganti@0 35 \
kkonganti@0 36  
kkonganti@0 37
kkonganti@0 38 #### `meta`
kkonganti@0 39
kkonganti@0 40 Type: Groovy Map
kkonganti@0 41
kkonganti@0 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@0 43
kkonganti@0 44 Ex:
kkonganti@0 45
kkonganti@0 46 ```groovy
kkonganti@0 47 [
kkonganti@0 48 id: 'FAL00870',
kkonganti@0 49 strandedness: 'unstranded',
kkonganti@0 50 single_end: true,
kkonganti@0 51 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@0 52 ]
kkonganti@0 53 ```
kkonganti@0 54
kkonganti@0 55 \
kkonganti@0 56  
kkonganti@0 57
kkonganti@0 58 #### `reads`
kkonganti@0 59
kkonganti@0 60 Type: `path`
kkonganti@0 61
kkonganti@0 62 NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run.
kkonganti@0 63
kkonganti@0 64 \
kkonganti@0 65  
kkonganti@0 66
kkonganti@0 67 #### `args`
kkonganti@0 68
kkonganti@0 69 Type: Groovy String
kkonganti@0 70
kkonganti@0 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@0 72
kkonganti@0 73 Ex:
kkonganti@0 74
kkonganti@0 75 ```groovy
kkonganti@0 76 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@0 77 ext.args = '--met 3'
kkonganti@0 78 }
kkonganti@0 79 ```
kkonganti@0 80
kkonganti@0 81 \
kkonganti@0 82  
kkonganti@0 83
kkonganti@0 84 ### `output:`
kkonganti@0 85
kkonganti@0 86 ___
kkonganti@0 87
kkonganti@0 88 Type: `tuple`
kkonganti@0 89
kkonganti@0 90 Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
kkonganti@0 91
kkonganti@0 92 \
kkonganti@0 93  
kkonganti@0 94
kkonganti@0 95 #### `report`
kkonganti@0 96
kkonganti@0 97 Type: `path`
kkonganti@0 98
kkonganti@0 99 NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
kkonganti@0 100
kkonganti@0 101 \
kkonganti@0 102  
kkonganti@0 103
kkonganti@0 104 #### `output`
kkonganti@0 105
kkonganti@0 106 Type: `path`
kkonganti@0 107
kkonganti@0 108 NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
kkonganti@0 109
kkonganti@0 110 \
kkonganti@0 111  
kkonganti@0 112
kkonganti@0 113 #### `kreport`
kkonganti@0 114
kkonganti@0 115 Type: `path`
kkonganti@0 116
kkonganti@0 117 NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
kkonganti@0 118
kkonganti@0 119 \
kkonganti@0 120  
kkonganti@0 121
kkonganti@0 122 #### `sam`
kkonganti@0 123
kkonganti@0 124 Type: `path`
kkonganti@0 125 \
kkonganti@0 126 Optional: `true`
kkonganti@0 127
kkonganti@0 128 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@0 129
kkonganti@0 130 \
kkonganti@0 131  
kkonganti@0 132
kkonganti@0 133 #### `fastq_mapped`
kkonganti@0 134
kkonganti@0 135 Type: `path`
kkonganti@0 136 \
kkonganti@0 137 Optional: `true`
kkonganti@0 138
kkonganti@0 139 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@0 140
kkonganti@0 141 \
kkonganti@0 142  
kkonganti@0 143
kkonganti@0 144 #### `fastq_unmapped`
kkonganti@0 145
kkonganti@0 146 Type: `path`
kkonganti@0 147 \
kkonganti@0 148 Optional: `true`
kkonganti@0 149
kkonganti@0 150 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@0 151
kkonganti@0 152 \
kkonganti@0 153  
kkonganti@0 154
kkonganti@0 155 #### `versions`
kkonganti@0 156
kkonganti@0 157 Type: `path`
kkonganti@0 158
kkonganti@0 159 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.