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

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 ABRICATE_RUN
5 ```
6
7 ## Description
8
9 Run `abricate` tool on a list of assembled contigs in FASTA format given a list of database names. Produces a single output table in ASCII text format per database.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`assembly`).
21
22 Ex:
23
24 ```groovy
25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
26 ```
27
28 \
29  
30
31 #### `meta`
32
33 Type: Groovy Map
34
35 A Groovy Map containing the metadata about the FASTQ file.
36
37 Ex:
38
39 ```groovy
40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
41 ```
42
43 \
44  
45
46 #### `assembly`
47
48 Type: `path`
49
50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
51
52 \
53  
54
55 #### `abdbs`
56
57 Type: `val`
58
59 Nextflow input type of `val` containing a list of at least one of the following database names on which `abricate` should be run.
60
61 Ex:
62
63 ```groovy
64 [ 'resfinder', 'megares', 'ncbi', 'ncbiamrplus', 'argannot' , 'ecoli_vf' ]
65 ```
66
67 \
68  
69
70 ### `output:`
71
72 ___
73
74 Type: `tuple`
75
76 Outputs a tuple of metadata (`meta` from `input:`) and list of `abricate` result files (`abricated`).
77
78 \
79  
80
81 #### `abricated`
82
83 Type: `path`
84
85 NextFlow output type of `path` pointing to the `abricate` results table file per sample (`id:`).
86
87 \
88  
89
90 #### `versions`
91
92 Type: `path`
93
94 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.