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1287ba48fe
* Update version & add intervals usage * Fix config when passing intervals as file * Use proper paths
62 lines
1.7 KiB
YAML
62 lines
1.7 KiB
YAML
name: deepvariant
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description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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keywords:
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- variant calling
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- machine learning
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tools:
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- deepvariant:
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description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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homepage: https://github.com/google/deepvariant
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documentation: https://github.com/google/deepvariant
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tool_dev_url: https://github.com/google/deepvariant
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doi: "https://doi.org/10.1038/nbt.4235"
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licence: ['BSD-3-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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- input:
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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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- index:
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type: file
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description: Index of BAM/CRAM file
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pattern: "*.bai/crai"
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- interval:
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type: file
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description: Interval file for targeted regions
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pattern: "*.bed"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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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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- vcf:
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type: file
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description: Compressed VCF file
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pattern: "*.vcf.gz"
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- gvcf:
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type: file
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description: Compressed GVCF file
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pattern: "*.g.vcf.gz"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@abhi18av"
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