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annotate 0.4.0/modules/abricate/summary/README.md @ 101:ce6d9548fe89

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author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # NextFlow DSL2 Module
kkonganti@101 2
kkonganti@101 3 ```bash
kkonganti@101 4 ABRICATE_SUMMARY
kkonganti@101 5 ```
kkonganti@101 6
kkonganti@101 7 ## Description
kkonganti@101 8
kkonganti@101 9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
kkonganti@101 10
kkonganti@101 11 \
kkonganti@101 12  
kkonganti@101 13
kkonganti@101 14 ### `input:`
kkonganti@101 15
kkonganti@101 16 ___
kkonganti@101 17
kkonganti@101 18 Type: `tuple`
kkonganti@101 19
kkonganti@101 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@101 21
kkonganti@101 22 Ex:
kkonganti@101 23
kkonganti@101 24 ```groovy
kkonganti@101 25 [
kkonganti@101 26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
kkonganti@101 27 [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@101 28 '/data/sample1/f.megares.ab.txt',
kkonganti@101 29 '/data/sample1/f.resfinder.ab.txt',
kkonganti@101 30 '/data/sample1/f.argannot.ab.txt',
kkonganti@101 31 '/data/sample1/f2.ncbi.ab.txt',
kkonganti@101 32 '/data/sample1/f2.megares.ab.txt',
kkonganti@101 33 '/data/sample1/f2.resfinder.ab.txt',
kkonganti@101 34 '/data/sample1/f2.argannot.ab.txt'
kkonganti@101 35 ]
kkonganti@101 36 ]
kkonganti@101 37 ```
kkonganti@101 38
kkonganti@101 39 \
kkonganti@101 40  
kkonganti@101 41
kkonganti@101 42 #### `abdbs`
kkonganti@101 43
kkonganti@101 44 Type: `val`
kkonganti@101 45
kkonganti@101 46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@101 47
kkonganti@101 48 Ex:
kkonganti@101 49
kkonganti@101 50 ```groovy
kkonganti@101 51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@101 52 ```
kkonganti@101 53
kkonganti@101 54 \
kkonganti@101 55  
kkonganti@101 56
kkonganti@101 57 #### `abfiles`
kkonganti@101 58
kkonganti@101 59 Type: `path`
kkonganti@101 60
kkonganti@101 61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@101 62
kkonganti@101 63 \
kkonganti@101 64  
kkonganti@101 65
kkonganti@101 66 ### `output:`
kkonganti@101 67
kkonganti@101 68 ___
kkonganti@101 69
kkonganti@101 70 #### `ncbi`
kkonganti@101 71
kkonganti@101 72 Type: `tuple`
kkonganti@101 73 \
kkonganti@101 74 Optional: `true`
kkonganti@101 75
kkonganti@101 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@101 77
kkonganti@101 78 \
kkonganti@101 79  
kkonganti@101 80
kkonganti@101 81 #### `ncbiamrplus`
kkonganti@101 82
kkonganti@101 83 Type: `tuple`
kkonganti@101 84 \
kkonganti@101 85 Optional: `true`
kkonganti@101 86
kkonganti@101 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@101 88
kkonganti@101 89 \
kkonganti@101 90  
kkonganti@101 91
kkonganti@101 92 #### `resfinder`
kkonganti@101 93
kkonganti@101 94 Type: `tuple`
kkonganti@101 95 \
kkonganti@101 96 Optional: `true`
kkonganti@101 97
kkonganti@101 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@101 99
kkonganti@101 100 \
kkonganti@101 101  
kkonganti@101 102
kkonganti@101 103 #### `megares`
kkonganti@101 104
kkonganti@101 105 Type: `tuple`
kkonganti@101 106 \
kkonganti@101 107 Optional: `true`
kkonganti@101 108
kkonganti@101 109 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@101 110
kkonganti@101 111 \
kkonganti@101 112  
kkonganti@101 113
kkonganti@101 114 #### `argannot`
kkonganti@101 115
kkonganti@101 116 Type: `tuple`
kkonganti@101 117 \
kkonganti@101 118 Optional: `true`
kkonganti@101 119
kkonganti@101 120 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@101 121
kkonganti@101 122 \
kkonganti@101 123  
kkonganti@101 124
kkonganti@101 125 #### `ecoli_vf`
kkonganti@101 126
kkonganti@101 127 Type: `tuple`
kkonganti@101 128 \
kkonganti@101 129 Optional: `true`
kkonganti@101 130
kkonganti@101 131 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@101 132
kkonganti@101 133 \
kkonganti@101 134  
kkonganti@101 135
kkonganti@101 136 #### `versions`
kkonganti@101 137
kkonganti@101 138 Type: `path`
kkonganti@101 139
kkonganti@101 140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.