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61 lines
1.8 KiB
YAML
61 lines
1.8 KiB
YAML
name: "svtk_standardize"
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description: Convert SV calls to a standardized format.
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keywords:
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- svtk
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- structural variants
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- SV
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- vcf
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- standardization
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tools:
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- "svtk":
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description: "Utilities for consolidating, filtering, resolving, and annotating structural variants."
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homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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doi: ""
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licence: "['MIT']"
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input:
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- args:
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type: map
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description: |
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Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.
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```
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{
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[
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"args": "",
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"caller": "delly" // Should be either delly, lumpy, manta, wham or melt
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]
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}
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```
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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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- vcf:
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type: file
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description: A gzipped VCF file to be standardized
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pattern: "*.vcf.gz"
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- fasta_fai:
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type: file
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description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
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pattern: "*.fai"
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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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- standardized_vcf:
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type: file
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description: A gzipped version of the standardized VCF file
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pattern: "*.std.vcf.gz"
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authors:
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- "@nvnieuwk"
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