Mercurial > repos > kkonganti > cfsan_bettercallsal

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
parents
children
comparison
equal deleted inserted replaced
16:b90e5a7a3d4f 17:0e7a0053e4a6
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.