mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
63 lines
1.7 KiB
YAML
63 lines
1.7 KiB
YAML
|
name: "hamronization_rgi"
|
||
|
|
description: Tool to convert and summarize RGI outputs using the hAMRonization specification.
|
||
|
|
keywords:
|
||
|
|
- amr
|
||
|
|
- antimicrobial resistance
|
||
|
|
- arg
|
||
|
|
- antimicrobial resistance genes
|
||
|
|
- reporting
|
||
|
|
- rgi
|
||
|
|
tools:
|
||
|
|
- hamronization:
|
||
|
|
description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
|
||
|
|
homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||
|
|
documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||
|
|
tool_dev_url: "https://github.com/pha4ge/hAMRonization"
|
||
|
|
doi: ""
|
||
|
|
licence: "['GNU Lesser General Public v3 (LGPL v3)']"
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- report:
|
||
|
|
type: file
|
||
|
|
description: Output .txt file from RGI
|
||
|
|
pattern: "*.txt"
|
||
|
|
- format:
|
||
|
|
type: value
|
||
|
|
description: Type of report file to be produced
|
||
|
|
pattern: "tsv|json"
|
||
|
|
- software_version:
|
||
|
|
type: value
|
||
|
|
description: Version of DeepARG used
|
||
|
|
pattern: "[0-9].[0-9].[0-9]"
|
||
|
|
- reference_db_version:
|
||
|
|
type: value
|
||
|
|
description: Database version of DeepARG used
|
||
|
|
pattern: "[0-9].[0-9].[0-9]"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
- json:
|
||
|
|
type: file
|
||
|
|
description: hAMRonised report in JSON format
|
||
|
|
pattern: "*.json"
|
||
|
|
- tsv:
|
||
|
|
type: file
|
||
|
|
description: hAMRonised report in TSV format
|
||
|
|
pattern: "*.json"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@louperelo"
|