mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
b6e4ecabba
* Bump pangolin version * Add nextclade to software list * Add nextclade module * Update md5sum for Pangolin due to version bump * Adding some URL to meta.yml * Adding new line at end of file Co-authored-by: JoseEspinosa <kadomu@gmail.com>
64 lines
1.8 KiB
YAML
Executable file
64 lines
1.8 KiB
YAML
Executable file
name: nextclade
|
|
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
|
|
keywords:
|
|
- nextclade
|
|
- variant
|
|
- consensus
|
|
tools:
|
|
- nextclade:
|
|
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
|
|
homepage: https://clades.nextstrain.org
|
|
documentation: None
|
|
tool_dev_url: https://github.com/nextstrain/nextclade
|
|
doi: ""
|
|
licence: ['MIT']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: FASTA file containing one or more consensus sequences
|
|
pattern: "*.{fasta,fa}"
|
|
- output_format:
|
|
type: string
|
|
description: |
|
|
String for output format supported by nextclade
|
|
i.e one of 'json', 'csv', 'tsv', 'tree', 'tsv-clades-only'
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
- csv:
|
|
type: file
|
|
description: CSV file containing nextclade results
|
|
pattern: "*.{csv}"
|
|
- json:
|
|
type: file
|
|
description: JSON file containing nextclade results
|
|
pattern: "*.{json}"
|
|
- json_tree:
|
|
type: file
|
|
description: Auspice JSON V2 containing nextclade results
|
|
pattern: "*.{tree.json}"
|
|
- tsv:
|
|
type: file
|
|
description: TSV file containing nextclade results
|
|
pattern: "*.{tsv}"
|
|
- tsv_clades:
|
|
type: file
|
|
description: TSV file containing nextclade results for clades only
|
|
pattern: "*.{clades.tsv}"
|
|
|
|
authors:
|
|
- "@drpatelh"
|