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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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1 # NextFlow DSL2 Module
2
3 ```bash
4 SALMON_INDEX
5 ```
6
7 ## Description
8
9 Run `salmon index` command on input FASTA file.
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` (`genome_fasta`) per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [
27 id: 'FAL00870'
28 ],
29 [
30 '/hpc/scratch/test/FAL00870_contigs.fasta',
31 ]
32 ]
33 ```
34
35 \
36  
37
38 #### `meta`
39
40 Type: Groovy Map
41
42 A Groovy Map containing the metadata about the genome FASTA file.
43
44 Ex:
45
46 ```groovy
47 [
48 id: 'FAL00870'
49 ]
50 ```
51
52 \
53  
54
55 #### `genome_fasta`
56
57 Type: `path`
58
59 NextFlow input type of `path` pointing to the FASTA file (gzipped or unzipped) on which `salmon index` should be run.
60
61 \
62  
63
64 ### `output:`
65
66 ___
67
68 Type: `tuple`
69
70 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon index` result files.
71
72 \
73  
74
75 #### `idx`
76
77 Type: `path`
78
79 NextFlow output type of `path` pointing to the `salmon index` result files per sample (`id:`).
80
81 \
82  
83
84 #### `versions`
85
86 Type: `path`
87
88 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.