2021-01-29 10:03:54 +00:00
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name: pangolin
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description: Phylogenetic Assignment of Named Global Outbreak LINeages
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keywords:
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2021-02-09 23:26:45 +00:00
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- covid
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- pangolin
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- lineage
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2021-01-29 10:03:54 +00:00
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tools:
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2021-02-09 23:26:45 +00:00
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- star:
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description: |
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Phylogenetic Assignment of Named Global Outbreak LINeages
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homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
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manual: https://github.com/cov-lineages/pangolin#pangolearn-description
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2021-01-29 10:03:54 +00:00
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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2021-01-29 10:03:54 +00:00
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input:
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2021-02-09 23:26:45 +00:00
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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- fasta:
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type: file
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description: |
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The genome assembly to be evaluated
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output:
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- report:
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type: file
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description: Pangolin lineage report
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pattern: "*.{csv}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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2021-01-29 10:03:54 +00:00
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authors:
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2021-02-09 23:26:45 +00:00
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- "@kevinmenden"
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- "@drpatelh"
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