nf-core_modules/software/snpeff/meta.yml
Maxime U. Garcia e0d820f9f4
Add snpeff (#546)
* feat: add snpeff

* fix: linting

* fix: tests

* fix: add csv output

* fix: add params information

* fix: improve script

* Update software/snpeff/environment.yml

* Update software/snpeff/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

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

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 13:40:55 +01:00

57 lines
1.6 KiB
YAML

name: snpEff
description: Genetic variant annotation and functional effect prediction toolbox
keywords:
- annotation
tools:
- snpeff:
description: |
SnpEff is a variant annotation and effect prediction tool.
It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
homepage: https://pcingola.github.io/SnpEff/
documentation: https://pcingola.github.io/SnpEff/se_introduction/
params:
- use_cache:
type: boolean
description: |
boolean to enable the usage of containers with cache
Enable the usage of containers with cache
Does not work with conda
- snpeff_tag:
type: value
description: |
Specify the tag for the container
https://hub.docker.com/r/nfcore/snpeff/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
- db:
type: value
description: |
which db to annotate with
- cache:
type: file
description: |
path to snpEff cache (optional)
output:
- vcf:
type: file
description: |
annotated vcf
pattern: "*.ann.vcf"
- report:
type: file
description: snpEff report file
pattern: "*.html"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@maxulysse"