mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 16:12:04 +00:00
7b4a28b6e8
* feat: add VEP module * fix: name * fix: EC lint] * feat: add info about params * fix: params as params, not input * fix: improve script * Update software/ensemblvep/environment.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
64 lines
1.8 KiB
YAML
64 lines
1.8 KiB
YAML
name: ENSEMBLVEP
|
|
description: Ensembl Variant Effect Predictor (VEP)
|
|
keywords:
|
|
- annotation
|
|
tools:
|
|
- ensemblvep:
|
|
description: |
|
|
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
|
|
or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
|
|
homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
|
|
documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
|
|
params:
|
|
- use_cache:
|
|
type: boolean
|
|
description: |
|
|
Enable the usage of containers with cache
|
|
Does not work with conda
|
|
- vep_tag:
|
|
type: value
|
|
description: |
|
|
Specify the tag for the container
|
|
https://hub.docker.com/r/nfcore/vep/tags
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- vcf:
|
|
type: file
|
|
description: |
|
|
vcf to annotate
|
|
- genome:
|
|
type: value
|
|
description: |
|
|
which genome to annotate with
|
|
- species:
|
|
type: value
|
|
description: |
|
|
which species to annotate with
|
|
- cache_version:
|
|
type: value
|
|
description: |
|
|
which version of the cache to annotate with
|
|
- cache:
|
|
type: file
|
|
description: |
|
|
path to VEP cache (optional)
|
|
output:
|
|
- vcf:
|
|
type: file
|
|
description: |
|
|
annotated vcf
|
|
pattern: "*.ann.vcf"
|
|
- report:
|
|
type: file
|
|
description: VEP report file
|
|
pattern: "*.html"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@maxulysse"
|