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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 KMA_ALIGN
5 ```
6
7 ## Description
8
9 Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
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 reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder per sample (`id:`).
21
22 Ex:
23
24 ```groovy
25 [
26 [
27 id: 'FAL00870',
28 strandedness: 'unstranded',
29 single_end: false
30 ],
31 [
32 '/hpc/scratch/test/f1.R1.fq.gz',
33 '/hpc/scratch/test/f1.R2.fq.gz'
34 ],
35 '/path/to/kma/index/folder'
36 ]
37 ```
38
39 \
40  
41
42 #### `meta`
43
44 Type: Groovy Map
45
46 A Groovy Map containing the metadata about the FASTQ file.
47
48 Ex:
49
50 ```groovy
51 [
52 id: 'FAL00870',
53 strandedness: 'unstranded',
54 single_end: true
55 ]
56 ```
57
58 \
59  
60
61 #### `reads`
62
63 Type: `path`
64
65 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
66
67 \
68  
69
70 #### `index`
71
72 Type: `path`
73
74 NextFlow input type of `path` pointing to folder containing `kma` index files.
75
76 \
77  
78
79 #### `args`
80
81 Type: Groovy String
82
83 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.
84
85 Ex:
86
87 ```groovy
88 withName: 'KMA_ALIGN' {
89 ext.args = '-mint2'
90 }
91 ```
92
93 ### `output:`
94
95 ___
96
97 Type: `tuple`
98
99 Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
100
101 \
102  
103
104 #### `res`
105
106 Type: `path`
107
108 NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
109
110 \
111  
112
113 #### `mapstat`
114
115 Type: `path`
116
117 NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
118
119 \
120  
121
122 #### `hits`
123
124 Type: `path`
125
126 NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
127
128 \
129  
130
131 #### `versions`
132
133 Type: `path`
134
135 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.