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c5634ba99b
* initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
62 lines
1.8 KiB
YAML
62 lines
1.8 KiB
YAML
name: bcftools_view
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description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
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keywords:
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- variant calling
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- view
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- bcftools
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- VCF
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tools:
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- view:
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description: |
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View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
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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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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 inspected.
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e.g. 'file.vcf'
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- index:
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type: file
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description: |
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The tab index for the VCF file to be inspected.
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e.g. 'file.tbi'
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- regions:
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type: file
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description: |
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Optionally, restrict the operation to regions listed in this file.
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e.g. 'file.vcf'
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- targets:
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type: file
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description: |
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Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
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e.g. 'file.vcf'
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- samples:
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type: file
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description: |
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Optional, file of sample names to be included or excluded.
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e.g. 'file.tsv'
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@abhi18av"
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