nf-core_modules/modules/vcf2maf/meta.yml
Adam Talbot f19ec865aa
vcf2maf module with built in VEP (#1768)
vcf2maf module created

Additions:
 - vcf2maf module created
 - If VEP is present in PATH, it is added to command
 - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
 - VEP version automatically added to versions.yml
 - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
 - Default Docker image includes VEP and vcf2maf
 - Test includes without VEP.

Relates to #490
2022-06-20 18:27:12 +02:00

47 lines
1.6 KiB
YAML

name: "vcf2maf"
description: vcf2maf
keywords:
- "vcf2maf"
- annotation
tools:
- "vcf2maf":
description: |
"Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF."
homepage: "https://github.com/mskcc/vcf2maf"
documentation: "https://github.com/mskcc/vcf2maf"
tool_dev_url: "https://github.com/mskcc/vcf2maf"
doi: "10.5281/zenodo.593251"
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 to convert to MAF format. Must be uncompressed.
- vep_cache:
type: file
description: |
Path to VEP cache dir. Required for correct running of VEP.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- maf:
type: file
description: MAF file produced from VCF
pattern: "*.maf"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@adamrtalbot"