mirror of
https://github.com/MillironX/nf-core_modules.git
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67 lines
2 KiB
YAML
67 lines
2 KiB
YAML
name: "happy_happy"
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description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.
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keywords:
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- happy
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- benchmark
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- haplotype
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tools:
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- "happy":
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description: "Haplotype VCF comparison tools"
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homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
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documentation: "https://github.com/Illumina/hap.py"
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tool_dev_url: "https://github.com/Illumina/hap.py"
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doi: ""
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licence: "['BSD-2-clause']"
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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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- truth_vcf:
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type: file
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description: gold standard VCF file
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pattern: "*.{vcf,vcf.gz}"
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- query_vcf:
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type: file
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description: VCF/GVCF file to query
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pattern: "*.{vcf,vcf.gz}"
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- bed:
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type: file
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description: BED file
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pattern: "*.bed"
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- fasta:
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type: file
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description: FASTA file of the reference genome
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pattern: "*.{fa,fasta}"
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- fasta_fai:
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type: file
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description: The index of the reference FASTA
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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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- summary:
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type: file
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description: A CSV file containing the summary of the benchmarking
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pattern: "*.summary.csv"
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- extended:
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type: file
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description: A CSV file containing extended info of the benchmarking
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pattern: "*.extended.csv"
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- runinfo:
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type: file
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description: A JSON file containing the run info
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pattern: "*.runinfo.json"
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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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- "@nvnieuwk"
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