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annotate 0.4.2/modules/abricate/summary/README.md @ 105:52045ea4679d

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