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author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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1 # NextFlow DSL2 Module
2
3 ```bash
4 SALMON_QUANT
5 ```
6
7 ## Description
8
9 Run `salmon quant` in `reads` or `alignments` mode. The inputs can be either the alignment (Ex: `.bam`) files or read (Ex: `.fastq.gz`) files.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `tuple`
19
20 Takes in the following tuple of metadata (`meta`) and either an alignment file or reads file and a `salmon index` or a transcript FASTA file per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [
27 id: 'FAL00870',
28 strandedness: 'unstranded',
29 single_end: true
30 ],
31 [
32 '/hpc/scratch/test/FAL00870_R1.fastq.gz'
33 ],
34 [
35 '/hpc/scratch/test/salmon_idx_for_FAL00870'
36 ]
37 ]
38 ```
39
40 \
41  
42
43 #### `meta`
44
45 Type: Groovy Map
46
47 A Groovy Map containing the metadata about the input setup for `salmon quant`.
48
49 Ex:
50
51 ```groovy
52 [
53 id: 'FAL00870',
54 strandedness: 'unstranded',
55 single_end: true
56 ]
57 ```
58
59 \
60  
61
62 #### `reads_or_bam`
63
64 Type: `path`
65
66 NextFlow input type of `path` pointing to either an alignment file (Ex: `.bam`) or a reads file (Ex: `.fastq.gz`) on which `salmon quant` should be run.
67
68 \
69  
70
71 #### `index_or_tr_fasta`
72
73 Type: `path`
74
75 NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
76
77 \
78  
79
80 #### `args`
81
82 Type: Groovy String
83
84 String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
85
86 Ex:
87
88 ```groovy
89 withName: 'SALMON_QUANT' {
90 ext.args = '--vbPrior 0.02'
91 }
92 ```
93
94 ### `output:`
95
96 ___
97
98 Type: `tuple`
99
100 Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon quant` result files.
101
102 \
103  
104
105 #### `results`
106
107 Type: `path`
108
109 NextFlow output type of `path` pointing to the `salmon quant` result files per sample (`id:`).
110
111 \
112  
113
114 #### `versions`
115
116 Type: `path`
117
118 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.