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annotate 0.3.0/modules/centrifuge/classify/README.md @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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kkonganti@92 1 # NextFlow DSL2 Module
kkonganti@92 2
kkonganti@92 3 ```bash
kkonganti@92 4 CENTRIFUGE_CLASSIFY
kkonganti@92 5 ```
kkonganti@92 6
kkonganti@92 7 ## Description
kkonganti@92 8
kkonganti@92 9 Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
kkonganti@92 10
kkonganti@92 11 \
kkonganti@92 12  
kkonganti@92 13
kkonganti@92 14 ### `input:`
kkonganti@92 15
kkonganti@92 16 ___
kkonganti@92 17
kkonganti@92 18 Type: `tuple`
kkonganti@92 19
kkonganti@92 20 Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@92 21
kkonganti@92 22 Ex:
kkonganti@92 23
kkonganti@92 24 ```groovy
kkonganti@92 25 [
kkonganti@92 26 [ id: 'FAL00870',
kkonganti@92 27 strandedness: 'unstranded',
kkonganti@92 28 single_end: true,
kkonganti@92 29 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@92 30 ],
kkonganti@92 31 '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@92 32 ]
kkonganti@92 33 ```
kkonganti@92 34
kkonganti@92 35 \
kkonganti@92 36  
kkonganti@92 37
kkonganti@92 38 #### `meta`
kkonganti@92 39
kkonganti@92 40 Type: Groovy Map
kkonganti@92 41
kkonganti@92 42 A Groovy Map containing the metadata about the FASTQ file.
kkonganti@92 43
kkonganti@92 44 Ex:
kkonganti@92 45
kkonganti@92 46 ```groovy
kkonganti@92 47 [
kkonganti@92 48 id: 'FAL00870',
kkonganti@92 49 strandedness: 'unstranded',
kkonganti@92 50 single_end: true,
kkonganti@92 51 centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@92 52 ]
kkonganti@92 53 ```
kkonganti@92 54
kkonganti@92 55 \
kkonganti@92 56  
kkonganti@92 57
kkonganti@92 58 #### `reads`
kkonganti@92 59
kkonganti@92 60 Type: `path`
kkonganti@92 61
kkonganti@92 62 NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run.
kkonganti@92 63
kkonganti@92 64 \
kkonganti@92 65  
kkonganti@92 66
kkonganti@92 67 #### `args`
kkonganti@92 68
kkonganti@92 69 Type: Groovy String
kkonganti@92 70
kkonganti@92 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@92 72
kkonganti@92 73 Ex:
kkonganti@92 74
kkonganti@92 75 ```groovy
kkonganti@92 76 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@92 77 ext.args = '--met 3'
kkonganti@92 78 }
kkonganti@92 79 ```
kkonganti@92 80
kkonganti@92 81 \
kkonganti@92 82  
kkonganti@92 83
kkonganti@92 84 ### `output:`
kkonganti@92 85
kkonganti@92 86 ___
kkonganti@92 87
kkonganti@92 88 Type: `tuple`
kkonganti@92 89
kkonganti@92 90 Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
kkonganti@92 91
kkonganti@92 92 \
kkonganti@92 93  
kkonganti@92 94
kkonganti@92 95 #### `report`
kkonganti@92 96
kkonganti@92 97 Type: `path`
kkonganti@92 98
kkonganti@92 99 NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
kkonganti@92 100
kkonganti@92 101 \
kkonganti@92 102  
kkonganti@92 103
kkonganti@92 104 #### `output`
kkonganti@92 105
kkonganti@92 106 Type: `path`
kkonganti@92 107
kkonganti@92 108 NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
kkonganti@92 109
kkonganti@92 110 \
kkonganti@92 111  
kkonganti@92 112
kkonganti@92 113 #### `kreport`
kkonganti@92 114
kkonganti@92 115 Type: `path`
kkonganti@92 116
kkonganti@92 117 NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
kkonganti@92 118
kkonganti@92 119 \
kkonganti@92 120  
kkonganti@92 121
kkonganti@92 122 #### `sam`
kkonganti@92 123
kkonganti@92 124 Type: `path`
kkonganti@92 125 \
kkonganti@92 126 Optional: `true`
kkonganti@92 127
kkonganti@92 128 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@92 129
kkonganti@92 130 \
kkonganti@92 131  
kkonganti@92 132
kkonganti@92 133 #### `fastq_mapped`
kkonganti@92 134
kkonganti@92 135 Type: `path`
kkonganti@92 136 \
kkonganti@92 137 Optional: `true`
kkonganti@92 138
kkonganti@92 139 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@92 140
kkonganti@92 141 \
kkonganti@92 142  
kkonganti@92 143
kkonganti@92 144 #### `fastq_unmapped`
kkonganti@92 145
kkonganti@92 146 Type: `path`
kkonganti@92 147 \
kkonganti@92 148 Optional: `true`
kkonganti@92 149
kkonganti@92 150 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@92 151
kkonganti@92 152 \
kkonganti@92 153  
kkonganti@92 154
kkonganti@92 155 #### `versions`
kkonganti@92 156
kkonganti@92 157 Type: `path`
kkonganti@92 158
kkonganti@92 159 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.