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50 lines
1.3 KiB
YAML
50 lines
1.3 KiB
YAML
name: expansionhunter
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description: Estimate repeat sizes using NGS data
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keywords:
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- STR
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- repeat_expansions
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tools:
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- expansionhunter:
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description: A tool for estimating repeat sizes
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homepage: https://github.com/Illumina/ExpansionHunter
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documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
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tool_dev_url: None
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doi: "10.1093/bioinformatics/btz431"
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licence: ["Apache-2.0"]
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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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- bam:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- fasta:
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type: file
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description: Reference genome
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pattern: "*.{fa,fasta}"
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- variant_catalog:
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type: file
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description: json file with repeat expansion sites to genotype
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pattern: "*.{json}"
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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', gender:'female' ]
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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 with repeat expansions
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pattern: "*.{vcf}"
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authors:
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- "@jemten"
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