nf-core_modules/modules/hamronization/abricate/meta.yml
Jasmin F 7f7f6bc913
Add module hamronization/abricate (#1925)
* Add hamronization/abricate

* Update input pattern in meta.yml

* Update location of hamronization test data

* Apply suggestions from code review
2022-07-26 12:55:53 +02:00

60 lines
1.8 KiB
YAML

name: "hamronization_abricate"
description: Tool to convert and summarize ABRicate outputs using the hAMRonization specification
keywords:
- amr
- antimicrobial resistance
- reporting
- abricate
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 TSV or CSV file from ABRicate
pattern: "*.{csv,tsv}"
- format:
type: value
description: Type of report file to be produced
pattern: "tsv|json"
- software_version:
type: value
description: Version of ABRicate used
pattern: "[0-9].[0-9].[0-9]"
- reference_db_version:
type: value
description: Database version of ABRicate used
pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[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:
- "@jasmezz"