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https://github.com/MillironX/nf-core_modules.git
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43a1c1c6d1
* Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
56 lines
1.6 KiB
YAML
56 lines
1.6 KiB
YAML
name: gatk4_variantfiltration
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description: Filter variants
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keywords:
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- vcf
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- filter
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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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']
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- vcf:
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type: list
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description: List of VCF(.gz) files
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pattern: "*.{vcf,vcf.gz}"
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- vcf_tbi:
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type: list
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description: List of VCF file indexes
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pattern: "*.{idx,tbi}"
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- fasta:
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type: file
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description: Fasta file of reference genome
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: Sequence dictionary of fastea file
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pattern: "*.dict"
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output:
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- vcf:
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type: file
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description: Compressed VCF file
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: Index of VCF file
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pattern: "*.vcf.gz.tbi"
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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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- "@kevinmenden"
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