mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
55 lines
1.6 KiB
YAML
55 lines
1.6 KiB
YAML
name: gatk4_combinegvcfs
|
|
description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
|
|
keywords:
|
|
- gvcf
|
|
- gatk4
|
|
- vcf
|
|
- combinegvcfs
|
|
- Short_Variant_Discovery
|
|
tools:
|
|
- gatk4:
|
|
description:
|
|
Genome Analysis Toolkit (GATK4). 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/articles/360037593911-CombineGVCFs
|
|
tool_dev_url: https://github.com/broadinstitute/gatk
|
|
doi: 10.1158/1538-7445.AM2017-3590
|
|
licence: ["Apache-2.0"]
|
|
|
|
input:
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
pattern: "*.fasta"
|
|
- fai:
|
|
type: file
|
|
description: FASTA index file
|
|
pattern: "*.{fai}"
|
|
- dict:
|
|
type: file
|
|
description: FASTA dictionary file
|
|
pattern: "*.{dict}"
|
|
- vcf:
|
|
type: file
|
|
description: Compressed VCF files
|
|
pattern: "*.vcf.gz"
|
|
- vcf_idx:
|
|
type: file
|
|
description: VCF Index file
|
|
pattern: "*.{fai}"
|
|
output:
|
|
- gvcf:
|
|
type: file
|
|
description: Compressed Combined GVCF file
|
|
pattern: "*.combined.g.vcf.gz"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@sateeshperi"
|
|
- "@mjcipriano"
|
|
- "@hseabolt"
|