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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
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description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
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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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licence: ["Apache-2.0"]
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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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- fasta:
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type: file
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description: |
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reference FASTA file (optional)
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pattern: "*.{fasta,fa}"
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- extra_files:
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type: tuple
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description: |
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path to file(s) needed for plugins (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 (optional)
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pattern: "*.ann.vcf"
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- tab:
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type: file
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description: |
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tab file with annotated variants (optional)
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pattern: "*.ann.tab"
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- json:
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type: file
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description: |
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json file with annotated variants (optional)
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pattern: "*.ann.json"
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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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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@maxulysse"
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