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56 lines
1.5 KiB
YAML
56 lines
1.5 KiB
YAML
name: cnvpytor_view
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description: view function to generate vcfs
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keywords:
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- cnv calling
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tools:
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- cnvpytor:
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description: calling CNVs using read depth
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homepage: https://github.com/abyzovlab/CNVpytor
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documentation: https://github.com/abyzovlab/CNVpytor
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tool_dev_url: https://github.com/abyzovlab/CNVpytor
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doi: "10.1101/2021.01.27.428472v1"
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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' ]
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- pytor_files:
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type: file
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description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
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pattern: "*.{pytor}"
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- bin_sizes:
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type: string
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description: list of binsizes separated by space e.g. "1000 10000" and "1000"
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- output_format:
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type: string
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description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"
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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' ]
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- tsv:
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type: file
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description: tsv file containing cnv calls
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pattern: "*.{tsv}"
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- vcf:
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type: file
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description: vcf file containing cnv calls
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pattern: "*.{vcf}"
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- xls:
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type: file
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description: xls file containing cnv calls
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pattern: "*.{xls}"
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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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authors:
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- "@sima-r"
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- "@ramprasadn"
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