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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
58 lines
1.5 KiB
YAML
58 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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params:
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- use_cache:
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type: boolean
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description: |
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boolean to enable the usage of containers with cache
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Enable the usage of containers with cache
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Does not work with conda
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- snpeff_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/snpeff/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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- 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 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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