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45 lines
1.4 KiB
YAML
45 lines
1.4 KiB
YAML
name: "manta_convertinversions"
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description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.
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keywords:
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- structural variants
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- conversion
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tools:
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- manta:
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description: Structural variant and indel caller for mapped sequencing data
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homepage: https://github.com/Illumina/manta
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documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
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tool_dev_url: https://github.com/Illumina/manta
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doi: "10.1093/bioinformatics/btv710"
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licence: ["GPL v3"]
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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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- vcf:
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type: file
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description: VCF file produces by Manta
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pattern: "*.vcf.gz"
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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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- vcf:
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type: file
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description: VCF file with reformatted inversions
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: TBI file produces by Manta
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pattern: "*.vcf.gz.tbi"
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authors:
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- "@FriederikeHanssen"
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