nf-core_modules/modules/hamronization/fargene/meta.yml
James A. Fellows Yates daab0a77dd
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-09-27 15:32:18 +02:00

62 lines
1.7 KiB
YAML

name: "hamronization_fargene"
description: Tool to convert and summarize fARGene outputs using the hAMRonization specification
keywords:
- amr
- antimicrobial resistance
- arg
- antimicrobial resistance genes
- reporting
- fARGene
tools:
- hamronization:
description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
homepage: "https://github.com/pha4ge/hAMRonization/"
documentation: "https://github.com/pha4ge/hAMRonization/"
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 fARGene
pattern: "*.txt"
- format:
type: value
description: Type of report file to be produced
pattern: "tsv|json"
- software_version:
type: value
description: Version of fARGene used
pattern: "[0-9].[0-9].[0-9]"
- reference_db_version:
type: value
description: Database version of fARGene 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:
- "@jfy133"