|
0
|
1 # NextFlow DSL2 Module
|
|
|
2
|
|
|
3 ```bash
|
|
|
4 SPADES_ASSEMBLE
|
|
|
5 ```
|
|
|
6
|
|
|
7 ## Description
|
|
|
8
|
|
|
9 Run `spades` 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 from various platforms of input type `path` (`illumina`, `pacbio`, `nanopore`).
|
|
|
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'], ['/data/sample1/nanopore.fastq'], ['/data/sample1/pacbio.fastq'] ]
|
|
|
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: 'FAL00870', strandedness: 'unstranded', single_end: true ]
|
|
|
42 ```
|
|
|
43
|
|
|
44 \
|
|
|
45
|
|
|
46
|
|
|
47 #### `illumina`
|
|
|
48
|
|
|
49 Type: `path`
|
|
|
50
|
|
|
51 NextFlow input type of `path` pointing to Illumina read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
|
|
|
52
|
|
|
53 \
|
|
|
54
|
|
|
55
|
|
|
56 #### `nanopore`
|
|
|
57
|
|
|
58 Type: `path`
|
|
|
59
|
|
|
60 NextFlow input type of `path` pointing to Oxford Nanopore read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
|
|
|
61
|
|
|
62 \
|
|
|
63
|
|
|
64
|
|
|
65 #### `pacbio`
|
|
|
66
|
|
|
67 Type: `path`
|
|
|
68
|
|
|
69 NextFlow input type of `path` pointing to PacBio read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any.
|
|
|
70
|
|
|
71 \
|
|
|
72
|
|
|
73
|
|
|
74 #### `args`
|
|
|
75
|
|
|
76 Type: Groovy String
|
|
|
77
|
|
|
78 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.
|
|
|
79
|
|
|
80 Ex:
|
|
|
81
|
|
|
82 ```groovy
|
|
|
83 withName: 'SPADES_ASSEMBLE' {
|
|
|
84 ext.args = '--rna'
|
|
|
85 }
|
|
|
86 ```
|
|
|
87
|
|
|
88 \
|
|
|
89
|
|
|
90
|
|
|
91 ### `output:`
|
|
|
92
|
|
|
93 ___
|
|
|
94
|
|
|
95 Type: `tuple`
|
|
|
96
|
|
|
97 Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format.
|
|
|
98
|
|
|
99 \
|
|
|
100
|
|
|
101
|
|
|
102 #### `assembly`
|
|
|
103
|
|
|
104 Type: `path`
|
|
|
105
|
|
|
106 NextFlow output type of `path` pointing to the `spades` assembler results file (`scaffolds.fasta`) per sample (`id:`) i.e., the final assembled scaffolds file in FASTA format.
|
|
|
107
|
|
|
108 \
|
|
|
109
|
|
|
110
|
|
|
111 #### `versions`
|
|
|
112
|
|
|
113 Type: `path`
|
|
|
114
|
|
|
115 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
|
