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annotate 0.7.0/modules/abricate/summary/README.md @ 19:4b304d77bbfb

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date Mon, 15 Jul 2024 11:20:22 -0400
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kkonganti@17 1 # NextFlow DSL2 Module
kkonganti@17 2
kkonganti@17 3 ```bash
kkonganti@17 4 ABRICATE_SUMMARY
kkonganti@17 5 ```
kkonganti@17 6
kkonganti@17 7 ## Description
kkonganti@17 8
kkonganti@17 9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
kkonganti@17 10
kkonganti@17 11 \
kkonganti@17 12  
kkonganti@17 13
kkonganti@17 14 ### `input:`
kkonganti@17 15
kkonganti@17 16 ___
kkonganti@17 17
kkonganti@17 18 Type: `tuple`
kkonganti@17 19
kkonganti@17 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@17 21
kkonganti@17 22 Ex:
kkonganti@17 23
kkonganti@17 24 ```groovy
kkonganti@17 25 [
kkonganti@17 26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
kkonganti@17 27 [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@17 28 '/data/sample1/f.megares.ab.txt',
kkonganti@17 29 '/data/sample1/f.resfinder.ab.txt',
kkonganti@17 30 '/data/sample1/f.argannot.ab.txt',
kkonganti@17 31 '/data/sample1/f2.ncbi.ab.txt',
kkonganti@17 32 '/data/sample1/f2.megares.ab.txt',
kkonganti@17 33 '/data/sample1/f2.resfinder.ab.txt',
kkonganti@17 34 '/data/sample1/f2.argannot.ab.txt'
kkonganti@17 35 ]
kkonganti@17 36 ]
kkonganti@17 37 ```
kkonganti@17 38
kkonganti@17 39 \
kkonganti@17 40  
kkonganti@17 41
kkonganti@17 42 #### `abdbs`
kkonganti@17 43
kkonganti@17 44 Type: `val`
kkonganti@17 45
kkonganti@17 46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@17 47
kkonganti@17 48 Ex:
kkonganti@17 49
kkonganti@17 50 ```groovy
kkonganti@17 51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@17 52 ```
kkonganti@17 53
kkonganti@17 54 \
kkonganti@17 55  
kkonganti@17 56
kkonganti@17 57 #### `abfiles`
kkonganti@17 58
kkonganti@17 59 Type: `path`
kkonganti@17 60
kkonganti@17 61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@17 62
kkonganti@17 63 \
kkonganti@17 64  
kkonganti@17 65
kkonganti@17 66 ### `output:`
kkonganti@17 67
kkonganti@17 68 ___
kkonganti@17 69
kkonganti@17 70 #### `ncbi`
kkonganti@17 71
kkonganti@17 72 Type: `tuple`
kkonganti@17 73 \
kkonganti@17 74 Optional: `true`
kkonganti@17 75
kkonganti@17 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@17 77
kkonganti@17 78 \
kkonganti@17 79  
kkonganti@17 80
kkonganti@17 81 #### `ncbiamrplus`
kkonganti@17 82
kkonganti@17 83 Type: `tuple`
kkonganti@17 84 \
kkonganti@17 85 Optional: `true`
kkonganti@17 86
kkonganti@17 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@17 88
kkonganti@17 89 \
kkonganti@17 90  
kkonganti@17 91
kkonganti@17 92 #### `resfinder`
kkonganti@17 93
kkonganti@17 94 Type: `tuple`
kkonganti@17 95 \
kkonganti@17 96 Optional: `true`
kkonganti@17 97
kkonganti@17 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@17 99
kkonganti@17 100 \
kkonganti@17 101  
kkonganti@17 102
kkonganti@17 103 #### `megares`
kkonganti@17 104
kkonganti@17 105 Type: `tuple`
kkonganti@17 106 \
kkonganti@17 107 Optional: `true`
kkonganti@17 108
kkonganti@17 109 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@17 110
kkonganti@17 111 \
kkonganti@17 112  
kkonganti@17 113
kkonganti@17 114 #### `argannot`
kkonganti@17 115
kkonganti@17 116 Type: `tuple`
kkonganti@17 117 \
kkonganti@17 118 Optional: `true`
kkonganti@17 119
kkonganti@17 120 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@17 121
kkonganti@17 122 \
kkonganti@17 123  
kkonganti@17 124
kkonganti@17 125 #### `ecoli_vf`
kkonganti@17 126
kkonganti@17 127 Type: `tuple`
kkonganti@17 128 \
kkonganti@17 129 Optional: `true`
kkonganti@17 130
kkonganti@17 131 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@17 132
kkonganti@17 133 \
kkonganti@17 134  
kkonganti@17 135
kkonganti@17 136 #### `versions`
kkonganti@17 137
kkonganti@17 138 Type: `path`
kkonganti@17 139
kkonganti@17 140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.