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annotate 0.6.1/modules/abricate/summary/README.md @ 13:74baf1a6c3bd

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 13:04:15 -0400
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kkonganti@11 1 # NextFlow DSL2 Module
kkonganti@11 2
kkonganti@11 3 ```bash
kkonganti@11 4 ABRICATE_SUMMARY
kkonganti@11 5 ```
kkonganti@11 6
kkonganti@11 7 ## Description
kkonganti@11 8
kkonganti@11 9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
kkonganti@11 10
kkonganti@11 11 \
kkonganti@11 12  
kkonganti@11 13
kkonganti@11 14 ### `input:`
kkonganti@11 15
kkonganti@11 16 ___
kkonganti@11 17
kkonganti@11 18 Type: `tuple`
kkonganti@11 19
kkonganti@11 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@11 21
kkonganti@11 22 Ex:
kkonganti@11 23
kkonganti@11 24 ```groovy
kkonganti@11 25 [
kkonganti@11 26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
kkonganti@11 27 [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@11 28 '/data/sample1/f.megares.ab.txt',
kkonganti@11 29 '/data/sample1/f.resfinder.ab.txt',
kkonganti@11 30 '/data/sample1/f.argannot.ab.txt',
kkonganti@11 31 '/data/sample1/f2.ncbi.ab.txt',
kkonganti@11 32 '/data/sample1/f2.megares.ab.txt',
kkonganti@11 33 '/data/sample1/f2.resfinder.ab.txt',
kkonganti@11 34 '/data/sample1/f2.argannot.ab.txt'
kkonganti@11 35 ]
kkonganti@11 36 ]
kkonganti@11 37 ```
kkonganti@11 38
kkonganti@11 39 \
kkonganti@11 40  
kkonganti@11 41
kkonganti@11 42 #### `abdbs`
kkonganti@11 43
kkonganti@11 44 Type: `val`
kkonganti@11 45
kkonganti@11 46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@11 47
kkonganti@11 48 Ex:
kkonganti@11 49
kkonganti@11 50 ```groovy
kkonganti@11 51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@11 52 ```
kkonganti@11 53
kkonganti@11 54 \
kkonganti@11 55  
kkonganti@11 56
kkonganti@11 57 #### `abfiles`
kkonganti@11 58
kkonganti@11 59 Type: `path`
kkonganti@11 60
kkonganti@11 61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@11 62
kkonganti@11 63 \
kkonganti@11 64  
kkonganti@11 65
kkonganti@11 66 ### `output:`
kkonganti@11 67
kkonganti@11 68 ___
kkonganti@11 69
kkonganti@11 70 #### `ncbi`
kkonganti@11 71
kkonganti@11 72 Type: `tuple`
kkonganti@11 73 \
kkonganti@11 74 Optional: `true`
kkonganti@11 75
kkonganti@11 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@11 77
kkonganti@11 78 \
kkonganti@11 79  
kkonganti@11 80
kkonganti@11 81 #### `ncbiamrplus`
kkonganti@11 82
kkonganti@11 83 Type: `tuple`
kkonganti@11 84 \
kkonganti@11 85 Optional: `true`
kkonganti@11 86
kkonganti@11 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@11 88
kkonganti@11 89 \
kkonganti@11 90  
kkonganti@11 91
kkonganti@11 92 #### `resfinder`
kkonganti@11 93
kkonganti@11 94 Type: `tuple`
kkonganti@11 95 \
kkonganti@11 96 Optional: `true`
kkonganti@11 97
kkonganti@11 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@11 99
kkonganti@11 100 \
kkonganti@11 101  
kkonganti@11 102
kkonganti@11 103 #### `megares`
kkonganti@11 104
kkonganti@11 105 Type: `tuple`
kkonganti@11 106 \
kkonganti@11 107 Optional: `true`
kkonganti@11 108
kkonganti@11 109 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@11 110
kkonganti@11 111 \
kkonganti@11 112  
kkonganti@11 113
kkonganti@11 114 #### `argannot`
kkonganti@11 115
kkonganti@11 116 Type: `tuple`
kkonganti@11 117 \
kkonganti@11 118 Optional: `true`
kkonganti@11 119
kkonganti@11 120 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@11 121
kkonganti@11 122 \
kkonganti@11 123  
kkonganti@11 124
kkonganti@11 125 #### `ecoli_vf`
kkonganti@11 126
kkonganti@11 127 Type: `tuple`
kkonganti@11 128 \
kkonganti@11 129 Optional: `true`
kkonganti@11 130
kkonganti@11 131 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@11 132
kkonganti@11 133 \
kkonganti@11 134  
kkonganti@11 135
kkonganti@11 136 #### `versions`
kkonganti@11 137
kkonganti@11 138 Type: `path`
kkonganti@11 139
kkonganti@11 140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.