|
0
|
1 # NextFlow DSL2 Module
|
|
|
2
|
|
|
3 ```bash
|
|
|
4 MLST
|
|
|
5 ```
|
|
|
6
|
|
|
7 ## Description
|
|
|
8
|
|
|
9 Run `mlst` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text 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 assemled contig FASTA files of input type `path` (`fasta`).
|
|
|
21
|
|
|
22 Ex:
|
|
|
23
|
|
|
24 ```groovy
|
|
|
25 [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
|
|
|
26 ```
|
|
|
27
|
|
|
28 \
|
|
|
29
|
|
|
30
|
|
|
31 #### `meta`
|
|
|
32
|
|
|
33 Type: Groovy Map
|
|
|
34
|
|
|
35 A Groovy Map containing the metadata about the FASTQ file.
|
|
|
36
|
|
|
37 Ex:
|
|
|
38
|
|
|
39 ```groovy
|
|
|
40 [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
|
|
|
41 ```
|
|
|
42
|
|
|
43 \
|
|
|
44
|
|
|
45
|
|
|
46 #### `fasta`
|
|
|
47
|
|
|
48 Type: `path`
|
|
|
49
|
|
|
50 NextFlow input type of `path` pointing to assembled contig file in FASTA format.
|
|
|
51
|
|
|
52 \
|
|
|
53
|
|
|
54
|
|
|
55 #### `args`
|
|
|
56
|
|
|
57 Type: Groovy String
|
|
|
58
|
|
|
59 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.
|
|
|
60
|
|
|
61 Ex:
|
|
|
62
|
|
|
63 ```groovy
|
|
|
64 withName: 'MLST' {
|
|
|
65 ext.args = '--nopath'
|
|
|
66 }
|
|
|
67 ```
|
|
|
68
|
|
|
69 \
|
|
|
70
|
|
|
71
|
|
|
72 ### `output:`
|
|
|
73
|
|
|
74 ___
|
|
|
75
|
|
|
76 Type: `tuple`
|
|
|
77
|
|
|
78 Outputs a tuple of metadata (`meta` from `input:`) and list of `mlst` result files (`tsv`).
|
|
|
79
|
|
|
80 \
|
|
|
81
|
|
|
82
|
|
|
83 #### `tsv`
|
|
|
84
|
|
|
85 Type: `path`
|
|
|
86
|
|
|
87 NextFlow output type of `path` pointing to the `mlst` results table file per sample (`id:`).
|
|
|
88
|
|
|
89 \
|
|
|
90
|
|
|
91
|
|
|
92 #### `versions`
|
|
|
93
|
|
|
94 Type: `path`
|
|
|
95
|
|
|
96 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
|
