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meta.yml
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meta.yml
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name: deepvariant
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
keywords:
- variant calling
- machine learning
- neural network
tools:
- deepvariant:
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
homepage: https://github.com/google/deepvariant
documentation: https://github.com/google/deepvariant
tool_dev_url: https://github.com/google/deepvariant
doi: "10.1038/nbt.4235"
licence: ["BSD-3-clause"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file
pattern: "*.bam/cram"
- index:
type: file
description: Index of BAM/CRAM file
pattern: "*.bai/crai"
- interval:
type: file
description: Interval file for targeted regions
pattern: "*.bed"
- meta2:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'genome' ]
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- meta3:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'genome' ]
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fai"
- meta4:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'genome' ]
- gzi:
type: file
description: GZI index of reference fasta file
pattern: "*.gzi"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
- gvcf:
type: file
description: Compressed GVCF file
pattern: "*.g.vcf.gz"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@abhi18av"
- "@ramprasadn"
maintainers:
- "@abhi18av"
- "@ramprasadn"