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comparison 0.7.0/modules/megahit/assemble/README.md @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 MEGAHIT_ASSEMBLE
5 ```
6
7 ## Description
8
9 Run `megahit` assembler tool on a list of read files in FASTQ format.
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 FASTQ files (short reads) of input type `path` (`reads`).
21
22 Ex:
23
24 ```groovy
25 [ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ]
26 [ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ]
27 ```
28
29 \
30  
31
32 #### `meta`
33
34 Type: Groovy Map
35
36 A Groovy Map containing the metadata about the FASTQ file.
37
38 Ex:
39
40 ```groovy
41 [ id: 'KB01', strandedness: 'unstranded', single_end: true ]
42 ```
43
44 \
45  
46
47 #### `reads`
48
49 Type: `path`
50
51 NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled.
52
53 \
54  
55
56 #### `args`
57
58 Type: Groovy String
59
60 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.
61
62 Ex:
63
64 ```groovy
65 withName: 'MEGAHIT_ASSEMBLE' {
66 ext.args = '--keep-tmp-files'
67 }
68 ```
69
70 \
71  
72
73 ### `output:`
74
75 ___
76
77 Type: `tuple`
78
79 Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format.
80
81 \
82  
83
84 #### `assembly`
85
86 Type: `path`
87
88 NextFlow output type of `path` pointing to the `megahit` assembler results file (`final.contigs.fa`) per sample (`id:`) i.e., the final assembled contigs file in FASTA format.
89
90 \
91  
92
93 #### `versions`
94
95 Type: `path`
96
97 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.