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annotate 0.2.1/modules/abricate/summary/README.md @ 22:0c42dc147b29

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author kkonganti
date Wed, 29 Jun 2022 09:38:17 -0400
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kkonganti@0 1 # NextFlow DSL2 Module
kkonganti@0 2
kkonganti@0 3 ```bash
kkonganti@0 4 ABRICATE_SUMMARY
kkonganti@0 5 ```
kkonganti@0 6
kkonganti@0 7 ## Description
kkonganti@0 8
kkonganti@0 9 Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
kkonganti@0 10
kkonganti@0 11 \
kkonganti@0 12  
kkonganti@0 13
kkonganti@0 14 ### `input:`
kkonganti@0 15
kkonganti@0 16 ___
kkonganti@0 17
kkonganti@0 18 Type: `tuple`
kkonganti@0 19
kkonganti@0 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@0 21
kkonganti@0 22 Ex:
kkonganti@0 23
kkonganti@0 24 ```groovy
kkonganti@0 25 [
kkonganti@0 26 [ 'megares', 'argannot', 'resfinder', 'ncbi' ],
kkonganti@0 27 [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@0 28 '/data/sample1/f.megares.ab.txt',
kkonganti@0 29 '/data/sample1/f.resfinder.ab.txt',
kkonganti@0 30 '/data/sample1/f.argannot.ab.txt',
kkonganti@0 31 '/data/sample1/f2.ncbi.ab.txt',
kkonganti@0 32 '/data/sample1/f2.megares.ab.txt',
kkonganti@0 33 '/data/sample1/f2.resfinder.ab.txt',
kkonganti@0 34 '/data/sample1/f2.argannot.ab.txt'
kkonganti@0 35 ]
kkonganti@0 36 ]
kkonganti@0 37 ```
kkonganti@0 38
kkonganti@0 39 \
kkonganti@0 40  
kkonganti@0 41
kkonganti@0 42 #### `abdbs`
kkonganti@0 43
kkonganti@0 44 Type: `val`
kkonganti@0 45
kkonganti@0 46 A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@0 47
kkonganti@0 48 Ex:
kkonganti@0 49
kkonganti@0 50 ```groovy
kkonganti@0 51 [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@0 52 ```
kkonganti@0 53
kkonganti@0 54 \
kkonganti@0 55  
kkonganti@0 56
kkonganti@0 57 #### `abfiles`
kkonganti@0 58
kkonganti@0 59 Type: `path`
kkonganti@0 60
kkonganti@0 61 NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@0 62
kkonganti@0 63 \
kkonganti@0 64  
kkonganti@0 65
kkonganti@0 66 ### `output:`
kkonganti@0 67
kkonganti@0 68 ___
kkonganti@0 69
kkonganti@0 70 #### `ncbi`
kkonganti@0 71
kkonganti@0 72 Type: `tuple`
kkonganti@0 73 \
kkonganti@0 74 Optional: `true`
kkonganti@0 75
kkonganti@0 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@0 77
kkonganti@0 78 \
kkonganti@0 79  
kkonganti@0 80
kkonganti@0 81 #### `ncbiamrplus`
kkonganti@0 82
kkonganti@0 83 Type: `tuple`
kkonganti@0 84 \
kkonganti@0 85 Optional: `true`
kkonganti@0 86
kkonganti@0 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@0 88
kkonganti@0 89 \
kkonganti@0 90  
kkonganti@0 91
kkonganti@0 92 #### `resfinder`
kkonganti@0 93
kkonganti@0 94 Type: `tuple`
kkonganti@0 95 \
kkonganti@0 96 Optional: `true`
kkonganti@0 97
kkonganti@0 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@0 99
kkonganti@0 100 \
kkonganti@0 101  
kkonganti@0 102
kkonganti@0 103 #### `megares`
kkonganti@0 104
kkonganti@0 105 Type: `tuple`
kkonganti@0 106 \
kkonganti@0 107 Optional: `true`
kkonganti@0 108
kkonganti@0 109 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@0 110
kkonganti@0 111 \
kkonganti@0 112  
kkonganti@0 113
kkonganti@0 114 #### `argannot`
kkonganti@0 115
kkonganti@0 116 Type: `tuple`
kkonganti@0 117 \
kkonganti@0 118 Optional: `true`
kkonganti@0 119
kkonganti@0 120 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@0 121
kkonganti@0 122 \
kkonganti@0 123  
kkonganti@0 124
kkonganti@0 125 #### `ecoli_vf`
kkonganti@0 126
kkonganti@0 127 Type: `tuple`
kkonganti@0 128 \
kkonganti@0 129 Optional: `true`
kkonganti@0 130
kkonganti@0 131 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@0 132
kkonganti@0 133 \
kkonganti@0 134  
kkonganti@0 135
kkonganti@0 136 #### `versions`
kkonganti@0 137
kkonganti@0 138 Type: `path`
kkonganti@0 139
kkonganti@0 140 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.