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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
64 lines
1.8 KiB
YAML
64 lines
1.8 KiB
YAML
name: ENSEMBLVEP
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description: Ensembl Variant Effect Predictor (VEP)
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keywords:
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- annotation
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tools:
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- ensemblvep:
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description: |
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VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
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or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
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homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
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documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
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params:
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- use_cache:
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type: boolean
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description: |
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Enable the usage of containers with cache
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Does not work with conda
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- vep_tag:
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type: value
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description: |
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Specify the tag for the container
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https://hub.docker.com/r/nfcore/vep/tags
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: |
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vcf to annotate
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- genome:
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type: value
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description: |
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which genome to annotate with
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- species:
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type: value
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description: |
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which species to annotate with
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- cache_version:
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type: value
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description: |
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which version of the cache to annotate with
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- cache:
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type: file
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description: |
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path to VEP cache (optional)
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output:
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- vcf:
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type: file
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description: |
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annotated vcf
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pattern: "*.ann.vcf"
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- report:
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type: file
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description: VEP report file
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pattern: "*.html"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@maxulysse"
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