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01d6d4c286
* Creation of Glimpse Chunk Add sub tools chunk with configuration and needed files for unitest. * Code linting correction * Prettier ran Newline deleted in nextflow.config * New final line and white spaces * Change Pytest.yml to work as a subtool. * Control for the parameters deleted. Control for the size/count of the window and buffer not needed. They have some defaults value. * Changed the different recommended part by @nvnieuwk Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
52 lines
1.6 KiB
YAML
52 lines
1.6 KiB
YAML
name: "glimpse_chunk"
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description: Defines chunks where to run imputation
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keywords:
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- chunk
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- imputation
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tools:
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- "glimpse":
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description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
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homepage: "https://odelaneau.github.io/GLIMPSE"
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documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
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tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
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doi: "10.1038/s41588-020-00756-0"
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licence: "['MIT']"
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input:
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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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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
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description: |
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Target dataset in VCF/BCF format defined at all variable positions.
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The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
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pattern: "*.{vcf,bcf}"
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- region:
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type: string
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description: |
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Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
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For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
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output:
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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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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- txt:
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type: file
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description: Tab delimited output txt file containing buffer and imputation regions.
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pattern: "*.{txt}"
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authors:
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- "@louislenezet"
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