mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
58 lines
1.6 KiB
YAML
58 lines
1.6 KiB
YAML
|
name: pangolin
|
||
|
|
description: Phylogenetic Assignment of Named Global Outbreak LINeages
|
||
|
|
keywords:
|
||
|
|
- covid
|
||
|
|
- pangolin
|
||
|
|
- lineage
|
||
|
|
tools:
|
||
|
|
- star:
|
||
|
|
description: |
|
||
|
|
Phylogenetic Assignment of Named Global Outbreak LINeages
|
||
|
|
homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
|
||
|
|
manual: https://github.com/cov-lineages/pangolin#pangolearn-description
|
||
|
|
params:
|
||
|
|
- outdir:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
The pipeline's output directory. By default, the module will
|
||
|
|
output files into `$params.outdir/<SOFTWARE>`
|
||
|
|
- publish_dir_mode:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
Value for the Nextflow `publishDir` mode parameter.
|
||
|
|
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||
|
|
- enable_conda:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Run the module with Conda using the software specified
|
||
|
|
via the `conda` directive
|
||
|
|
- singularity_pull_docker_container:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Instead of directly downloading Singularity images for use with Singularity,
|
||
|
|
force the workflow to pull and convert Docker containers instead.
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
- assembly:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
The virus genome assembly to be evaluated
|
||
|
|
|
||
|
|
output:
|
||
|
|
- lineage_report:
|
||
|
|
type: file
|
||
|
|
description: The lineage report
|
||
|
|
pattern: "{prefix}.lineage_report.csv"
|
||
|
|
|
||
|
|
- version:
|
||
|
|
type: file
|
||
|
|
description: File containing software version
|
||
|
|
pattern: "*.{version.txt}"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@kevinmenden"
|