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6243c3792c
* Add stubs for deepvariant [ci skip] * Update the stubs for deepvariant [ci skip] * functional with google docker image * cleanup * consume docker container within singularity executor * update the meta.yml file and ask for review * tweak the input channel shape and test data * tweak input data [ci skip] * update for the new syntax * remove the functions and rename meta vars * Update the arguments mechanism * update chr, region and checksum Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
58 lines
1.6 KiB
YAML
58 lines
1.6 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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- bam:
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type: file
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description: BAM file
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pattern: "*.bam"
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- bai:
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type: file
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description: Index of BAM file
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pattern: "*.bai"
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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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