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comparison 0.4.0/modules/spades/assemble/README.md @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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100:9d9537c907bd 101:ce6d9548fe89
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.