mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
60 lines
1.7 KiB
YAML
60 lines
1.7 KiB
YAML
name: nextclade_run
|
|
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
|
|
keywords:
|
|
- nextclade
|
|
- variant
|
|
- consensus
|
|
tools:
|
|
- nextclade:
|
|
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
|
|
homepage: https://github.com/nextstrain/nextclade
|
|
documentation: https://github.com/nextstrain/nextclade
|
|
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 ]
|
|
- dataset:
|
|
type: path
|
|
description: Path containing the dataset files obtained by running nextclade dataset get
|
|
pattern: "*"
|
|
- fasta:
|
|
type: file
|
|
description: FASTA file containing one or more consensus sequences
|
|
pattern: "*.{fasta,fa}"
|
|
|
|
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"
|
|
- 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}"
|
|
|
|
authors:
|
|
- "@antunderwood"
|
|
- "@drpatelh"
|