nf-core_modules/modules/bcftools/index/meta.yml

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name: bcftools_index
description: Index VCF tools
keywords:
- vcf
- index
- bcftools
- csi
- tbi
tools:
- bcftools:
description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
homepage: https://samtools.github.io/bcftools/
documentation: https://samtools.github.io/bcftools/howtos/index.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/gigascience/giab008"
licence: ['MIT', 'GPL-3.0-or-later']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- VCF:
type: file
description: VCF file (optionally GZIPPED)
pattern: "*.{vcf,vcf.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "versions.yml"
- csi:
type: file
description: Default VCF file index file
pattern: "*.csi"
- tbi:
type: file
description: Alternative VCF file index file for larger files (activated with -t parameter)
pattern: "*.tbi"
authors:
- "@jfy133"