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comparison 0.7.0/modules/abricate/summary/README.md @ 17:0e7a0053e4a6

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