mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
30f72e2482
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774 * Trying to fix tests * Still trying to fix tests * Fetching the vep-output-file-extension from the args. * Update meta.yml * WIP: Adding tests for vep-output json and tab * updated the test.yml Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
73 lines
2 KiB
YAML
73 lines
2 KiB
YAML
name: ENSEMBLVEP
|
|
description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
|
|
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
|
|
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 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)
|
|
- fasta:
|
|
type: file
|
|
description: |
|
|
reference FASTA file (optional)
|
|
pattern: "*.{fasta,fa}"
|
|
- extra_files:
|
|
type: tuple
|
|
description: |
|
|
path to file(s) needed for plugins (optional)
|
|
output:
|
|
- vcf:
|
|
type: file
|
|
description: |
|
|
annotated vcf (optional)
|
|
pattern: "*.ann.vcf"
|
|
- tab:
|
|
type: file
|
|
description: |
|
|
tab file with annotated variants (optional)
|
|
pattern: "*.ann.tab"
|
|
- json:
|
|
type: file
|
|
description: |
|
|
json file with annotated variants (optional)
|
|
pattern: "*.ann.json"
|
|
- report:
|
|
type: file
|
|
description: VEP report file
|
|
pattern: "*.html"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@maxulysse"
|