mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
61 lines
1.7 KiB
YAML
61 lines
1.7 KiB
YAML
|
name: hamronization_deeparg
|
||
|
|
description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
|
||
|
|
keywords:
|
||
|
|
- amr
|
||
|
|
- antimicrobial resistance
|
||
|
|
- reporting
|
||
|
|
- deeparg
|
||
|
|
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 .mapping.ARG file from DeepARG
|
||
|
|
pattern: "*.mapping.ARG"
|
||
|
|
- 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]"
|
||
|
|
|
||
|
|
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:
|
||
|
|
- "@jfy133"
|