nf-core_modules/modules/svtk/standardize/meta.yml
nvnieuwk bf09fdf892
new module: svtk/standardize (#2031)
* new module: svtk/standardize

* linting

* fixed tests
2022-09-08 15:03:08 +02:00

61 lines
1.8 KiB
YAML

name: "svtk_standardize"
description: Convert SV calls to a standardized format.
keywords:
- svtk
- structural variants
- SV
- vcf
- standardization
tools:
- "svtk":
description: "Utilities for consolidating, filtering, resolving, and annotating structural variants."
homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
doi: ""
licence: "['MIT']"
input:
- args:
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.
```
{
[
"args": "",
"caller": "delly" // Should be either delly, lumpy, manta, wham or melt
]
}
```
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: A gzipped VCF file to be standardized
pattern: "*.vcf.gz"
- fasta_fai:
type: file
description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
pattern: "*.fai"
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"
- standardized_vcf:
type: file
description: A gzipped version of the standardized VCF file
pattern: "*.std.vcf.gz"
authors:
- "@nvnieuwk"