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annotate 0.4.0/modules/centrifuge/classify/README.md @ 101:ce6d9548fe89

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