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comparison 0.5.0/modules/kma/index/README.md @ 1:365849f031fd

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author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 # NextFlow DSL2 Module
2
3 ```bash
4 KMA_INDEX
5 ```
6
7 ## Description
8
9 Run `kma index` alinger on input FASTA files.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following tuple of metadata (`meta`) and a FASTA file of type `path` (`fasta`) per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [
27 id: 'FAL00870',
28 ],
29 '/path/to/FAL00870_contigs.fasta'
30 ]
31 ```
32
33 \
34  
35
36 #### `meta`
37
38 Type: Groovy Map
39
40 A Groovy Map containing the metadata about the FASTA file.
41
42 Ex:
43
44 ```groovy
45 [
46 id: 'FAL00870'
47 ]
48 ```
49
50 \
51  
52
53 #### `fasta`
54
55 Type: `path`
56
57 NextFlow input type of `path` pointing to the FASTA file on which the `kma index` command should be run.
58
59 \
60  
61
62 ### `output:`
63
64 ___
65
66 Type: `tuple`
67
68 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `kma index` files.
69
70 \
71  
72
73 #### `idx`
74
75 Type: `path`
76
77 NextFlow output type of `path` pointing to the folder containing `kma index` files per sample (`id:`).
78
79 \
80  
81
82 #### `versions`
83
84 Type: `path`
85
86 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.