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Tidy up

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drpatelh 2021-02-09 23:26:45 +00:00
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software/pangolin/meta.yml
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@ -1,57 +1,54 @@
name: pangolin name: pangolin
description: Phylogenetic Assignment of Named Global Outbreak LINeages description: Phylogenetic Assignment of Named Global Outbreak LINeages
keywords: keywords:
- covid - covid
- pangolin - pangolin
- lineage - lineage
tools: tools:
- star: - star:
description: | description: |
Phylogenetic Assignment of Named Global Outbreak LINeages Phylogenetic Assignment of Named Global Outbreak LINeages
homepage: https://github.com/cov-lineages/pangolin#pangolearn-description homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
manual: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description
params: params:
- outdir: - outdir:
type: string type: string
description: | description: |
The pipeline's output directory. By default, the module will The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>` output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode: - publish_dir_mode:
type: string type: string
description: | description: |
Value for the Nextflow `publishDir` mode parameter. Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move. Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda: - enable_conda:
type: boolean type: boolean
description: | description: |
Run the module with Conda using the software specified Run the module with Conda using the software specified
via the `conda` directive via the `conda` directive
- singularity_pull_docker_container: - singularity_pull_docker_container:
type: boolean type: boolean
description: | description: |
Instead of directly downloading Singularity images for use with Singularity, Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead. force the workflow to pull and convert Docker containers instead.
input: input:
- meta: - meta:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
- fasta: - fasta:
type: file type: file
description: | description: |
The genome assembly to be evaluated The genome assembly to be evaluated
output: output:
- report: - report:
type: file type: file
description: The lineage report description: Pangolin lineage report
pattern: "{prefix}.lineage_report.csv" pattern: "*.{csv}"
- version:
- version: type: file
type: file description: File containing software version
description: File containing software version pattern: "*.{version.txt}"
pattern: "*.{version.txt}"
authors: authors:
- "@kevinmenden" - "@kevinmenden"
- "@drpatelh"