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drpatelh 2021-02-09 23:26:45 +00:00
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name: pangolin
description: Phylogenetic Assignment of Named Global Outbreak LINeages
keywords:
- covid
- pangolin
- lineage
- 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
- 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 `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$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
- fasta:
type: file
description: |
The genome assembly to be evaluated
- meta:
type: map
description: |
Groovy Map containing sample information
- fasta:
type: file
description: |
The genome assembly to be evaluated
output:
- report:
type: file
description: The lineage report
pattern: "{prefix}.lineage_report.csv"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- report:
type: file
description: Pangolin lineage report
pattern: "*.{csv}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"
- "@kevinmenden"
- "@drpatelh"