mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
72 lines
2.1 KiB
YAML
72 lines
2.1 KiB
YAML
name: "gatk4_cnnscorevariants"
|
|
description: Apply a Convolutional Neural Net to filter annotated variants
|
|
keywords:
|
|
- gatk4_cnnscorevariants
|
|
- gatk4
|
|
- variants
|
|
tools:
|
|
- gatk4:
|
|
description: |
|
|
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
|
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
|
and high-performance computing features make it capable of taking on projects of any size.
|
|
homepage: https://gatk.broadinstitute.org/hc/en-us
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
|
doi: 10.1158/1538-7445.AM2017-3590
|
|
licence: ["Apache-2.0"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- vcf:
|
|
type: file
|
|
description: VCF file
|
|
pattern: "*.vcf.gz"
|
|
- aligned_input:
|
|
type: file
|
|
description: BAM/CRAM file from alignment (optional)
|
|
pattern: "*.{bam,cram}"
|
|
- intervals:
|
|
type: file
|
|
description: Bed file with the genomic regions included in the library (optional)
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
pattern: "*.fasta"
|
|
- fai:
|
|
type: file
|
|
description: Index of reference fasta file
|
|
pattern: "*.fasta.fai"
|
|
- dict:
|
|
type: file
|
|
description: GATK sequence dictionary
|
|
pattern: "*.dict"
|
|
- architecture:
|
|
type: file
|
|
description: Neural Net architecture configuration json file (optional)
|
|
pattern: "*.json"
|
|
- weights:
|
|
type: file
|
|
description: Keras model HD5 file with neural net weights. (optional)
|
|
pattern: "*.hd5"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- vcf:
|
|
type: file
|
|
description: Annotated VCF file
|
|
pattern: "*.vcf"
|
|
|
|
authors:
|
|
- "@FriederikeHanssen"
|