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annotate 0.3.0/modules/abricate/summary/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 ABRICATE_SUMMARY
kkonganti@92 5 ```
kkonganti@92 6
kkonganti@92 7 ## Description
kkonganti@92 8
kkonganti@92 9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
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 `abricate` database names of type `val` (`abdbs`) and a list of `abricate` result table files for all databases of type `path` (`abfiles`).
kkonganti@92 21
kkonganti@92 22 Ex:
kkonganti@92 23
kkonganti@92 24 ```groovy
kkonganti@92 25 [
kkonganti@92 26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
kkonganti@92 27 [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@92 28 '/data/sample1/f.megares.ab.txt',
kkonganti@92 29 '/data/sample1/f.resfinder.ab.txt',
kkonganti@92 30 '/data/sample1/f.argannot.ab.txt',
kkonganti@92 31 '/data/sample1/f2.ncbi.ab.txt',
kkonganti@92 32 '/data/sample1/f2.megares.ab.txt',
kkonganti@92 33 '/data/sample1/f2.resfinder.ab.txt',
kkonganti@92 34 '/data/sample1/f2.argannot.ab.txt'
kkonganti@92 35 ]
kkonganti@92 36 ]
kkonganti@92 37 ```
kkonganti@92 38
kkonganti@92 39 \
kkonganti@92 40  
kkonganti@92 41
kkonganti@92 42 #### `abdbs`
kkonganti@92 43
kkonganti@92 44 Type: `val`
kkonganti@92 45
kkonganti@92 46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@92 47
kkonganti@92 48 Ex:
kkonganti@92 49
kkonganti@92 50 ```groovy
kkonganti@92 51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@92 52 ```
kkonganti@92 53
kkonganti@92 54 \
kkonganti@92 55  
kkonganti@92 56
kkonganti@92 57 #### `abfiles`
kkonganti@92 58
kkonganti@92 59 Type: `path`
kkonganti@92 60
kkonganti@92 61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@92 62
kkonganti@92 63 \
kkonganti@92 64  
kkonganti@92 65
kkonganti@92 66 ### `output:`
kkonganti@92 67
kkonganti@92 68 ___
kkonganti@92 69
kkonganti@92 70 #### `ncbi`
kkonganti@92 71
kkonganti@92 72 Type: `tuple`
kkonganti@92 73 \
kkonganti@92 74 Optional: `true`
kkonganti@92 75
kkonganti@92 76 Outputs a tuple of `abricate` database key (`abricate_ncbi`) and summary result file from `abricate summary` command of type `path` (`ncbi`). This database includes only core AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbi.absum.txt`
kkonganti@92 77
kkonganti@92 78 \
kkonganti@92 79  
kkonganti@92 80
kkonganti@92 81 #### `ncbiamrplus`
kkonganti@92 82
kkonganti@92 83 Type: `tuple`
kkonganti@92 84 \
kkonganti@92 85 Optional: `true`
kkonganti@92 86
kkonganti@92 87 Outputs a tuple of `abricate` database key (`abricate_ncbiamrplus`) and summary result file from `abricate summary` command of type `path` (`ncbiamrplus`). This database includes both core AMR genes and plus AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbiamrplus.absum.txt`
kkonganti@92 88
kkonganti@92 89 \
kkonganti@92 90  
kkonganti@92 91
kkonganti@92 92 #### `resfinder`
kkonganti@92 93
kkonganti@92 94 Type: `tuple`
kkonganti@92 95 \
kkonganti@92 96 Optional: `true`
kkonganti@92 97
kkonganti@92 98 Outputs a tuple of `abricate` database key (`abricate_resfinder`) and summary result file from `abricate summary` command of type `path` (`resfinder`). This tuple is emitted optionally only where there are output files with suffix `.resfinder.absum.txt`
kkonganti@92 99
kkonganti@92 100 \
kkonganti@92 101  
kkonganti@92 102
kkonganti@92 103 #### `megares`
kkonganti@92 104
kkonganti@92 105 Type: `tuple`
kkonganti@92 106 \
kkonganti@92 107 Optional: `true`
kkonganti@92 108
kkonganti@92 109 Outputs a tuple of `abricate` database key (`abricate_megares`) and summary result file from `abricate summary` command of type `path` (`megares`). This tuple is emitted optionally only where there are output files with suffix `.megares.absum.txt`
kkonganti@92 110
kkonganti@92 111 \
kkonganti@92 112  
kkonganti@92 113
kkonganti@92 114 #### `argannot`
kkonganti@92 115
kkonganti@92 116 Type: `tuple`
kkonganti@92 117 \
kkonganti@92 118 Optional: `true`
kkonganti@92 119
kkonganti@92 120 Outputs a tuple of `abricate` database key (`abricate_argannot`) and summary result file from `abricate summary` command of type `path` (`argannot`). This tuple is emitted optionally only where there are output files with suffix `.argannot.absum.txt`
kkonganti@92 121
kkonganti@92 122 \
kkonganti@92 123  
kkonganti@92 124
kkonganti@92 125 #### `ecoli_vf`
kkonganti@92 126
kkonganti@92 127 Type: `tuple`
kkonganti@92 128 \
kkonganti@92 129 Optional: `true`
kkonganti@92 130
kkonganti@92 131 Outputs an **optional** tuple of `abricate` database key (`abricate_ecoli_vf`) and summary result file from `abricate summary` command of type `path` (`ecoli_vf`). This tuple is emitted only when there are output files with suffix `.ecoli_vf.absum.txt` within the `work` folder.
kkonganti@92 132
kkonganti@92 133 \
kkonganti@92 134  
kkonganti@92 135
kkonganti@92 136 #### `versions`
kkonganti@92 137
kkonganti@92 138 Type: `path`
kkonganti@92 139
kkonganti@92 140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.