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ffe0375048
* Extending output from snpEff * Test of additional output-files from snpEff * Removing some md5 checks
54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
name: snpEff
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description: Genetic variant annotation and functional effect prediction toolbox
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keywords:
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- annotation
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tools:
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- snpeff:
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description: |
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SnpEff is a variant annotation and effect prediction tool.
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It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
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homepage: https://pcingola.github.io/SnpEff/
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documentation: https://pcingola.github.io/SnpEff/se_introduction/
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licence: ["MIT"]
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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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- db:
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type: value
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description: |
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which db 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 snpEff 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: snpEff report csv file
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pattern: "*.csv"
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- summary_html:
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type: file
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description: snpEff summary statistics in html file
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pattern: "*.html"
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- genes_txt:
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type: file
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description: txt (tab separated) file having counts of the number of variants affecting each transcript and gene
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pattern: "*.genes.txt"
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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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