mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
a25423dbb9
* add gatk4/combinegvcfs module * update gatk4/combinegvcfs * loop to create a string adding -V to each vcf file * add contains for variable md5 * rm whitespace * meta in output * fix indentations * fix indentations * move tmpdir to args and update conda version Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
54 lines
1.6 KiB
YAML
54 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"
|