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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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1 # NextFlow DSL2 Module
2
3 ```bash
4 BBTOOLS_BBMERGE
5 ```
6
7 ## Description
8
9 Run `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection.
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`) 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 ]
36 ```
37
38 \
39  
40
41 #### `meta`
42
43 Type: Groovy Map
44
45 A Groovy Map containing the metadata about the FASTQ file.
46
47 Ex:
48
49 ```groovy
50 [
51 id: 'FAL00870',
52 strandedness: 'unstranded',
53 single_end: true
54 ]
55 ```
56
57 \
58  
59
60 #### `reads`
61
62 Type: `path`
63
64 NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
65
66 \
67  
68
69 #### `args`
70
71 Type: Groovy String
72
73 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.
74
75 Ex:
76
77 ```groovy
78 withName: 'BBTOOLS_BBMERGE' {
79 ext.args = 'minprog=0.5'
80 }
81 ```
82
83 ### `output:`
84
85 ___
86
87 Type: `tuple`
88
89 Outputs a tuple of metadata (`meta` from `input:`) and merged gzipped FASTQ file.
90
91 \
92  
93
94 #### `fastq`
95
96 Type: `path`
97
98 NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`).
99
100 \
101  
102
103 #### `log`
104
105 Type: `path`
106
107 NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`).
108
109 \
110  
111
112 #### `versions`
113
114 Type: `path`
115
116 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.