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comparison 0.4.2/modules/amrfinderplus/run/README.md @ 130:04f6ac8ca13c

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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
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1 # NextFlow DSL2 Module
2
3 ```bash
4 AMRFINDERPLUS_RUN
5 ```
6
7 ## Description
8
9 Run `amrfinder` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format per database.
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 file 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, organism: 'Escherichia' ]
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: 'AMRFINDERPLUS_RUN' {
65 ext.args = '--gpipe_org'
66 }
67 ```
68
69 ### `output:`
70
71 ___
72
73 Type: `tuple`
74
75 Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
76
77 \
78  
79
80 #### `report`
81
82 Type: `path`
83
84 NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
85
86 \
87  
88
89 #### `mutional_report`
90
91 Type: `path`
92 \
93 Optional: `true`
94
95 NextFlow output type of `path` pointing to the `amrfinder` mutation results table file (`.tsv`) per sample (`id:`). Obtaining this output will depend on the presence of the `organism` key in the metadata (`meta`). See example above.
96
97 \
98  
99
100 #### `versions`
101
102 Type: `path`
103
104 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.