mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
74 lines
2.1 KiB
YAML
74 lines
2.1 KiB
YAML
name: "gatk4_reblockgvcf"
|
|
description: Condenses homRef blocks in a single-sample GVCF
|
|
keywords:
|
|
- gatk4
|
|
- reblockgvcf
|
|
- gvcf
|
|
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 ]
|
|
- gvcf:
|
|
type: file
|
|
description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode
|
|
pattern: "*.{vcf,gvcf}.gz"
|
|
- tbi:
|
|
type: file
|
|
description: Index of the GVCF file
|
|
pattern: "*.tbi"
|
|
- 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"
|
|
- dbsnp:
|
|
type: file
|
|
description: VCF file containing known sites (optional)
|
|
- dbsnp_tbi:
|
|
type: file
|
|
description: VCF index of dbsnp (optional)
|
|
|
|
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"
|
|
- gvcf:
|
|
type: file
|
|
description: Filtered GVCF
|
|
pattern: "*reblock.g.vcf.gz"
|
|
- tbi:
|
|
type: file
|
|
description: Index of the filtered GVCF
|
|
pattern: "*reblock.g.vcf.gz.tbi"
|
|
|
|
authors:
|
|
- "@nvnieuwk"
|