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d596571a03
* added an optional vcf index to bcftools/norm * updated test.yml for failing conda tests
52 lines
1.3 KiB
YAML
52 lines
1.3 KiB
YAML
name: bcftools_norm
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description: Normalize VCF file
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keywords:
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- normalize
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- norm
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- variant calling
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- VCF
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tools:
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- norm:
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description: |
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Normalize VCF files.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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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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The vcf file to be normalized
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e.g. 'file1.vcf'
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pattern: "*.{vcf,vcf.gz}"
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- tbi:
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type: file
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description: |
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An optional index of the VCF file (for when the VCF is compressed)
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pattern: "*.vcf.gz.tbi"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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output:
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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: VCF normalized output file
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pattern: "*.vcf.gz"
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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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- "@abhi18av"
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