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https://github.com/MillironX/nf-core_modules.git
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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>
49 lines
1.6 KiB
YAML
49 lines
1.6 KiB
YAML
name: bcftools_index
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description: Index VCF tools
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keywords:
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- vcf
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- index
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- bcftools
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- csi
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- tbi
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tools:
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- bcftools:
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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.
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homepage: https://samtools.github.io/bcftools/
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documentation: https://samtools.github.io/bcftools/howtos/index.html
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tool_dev_url: https://github.com/samtools/bcftools
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doi: "10.1093/gigascience/giab008"
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licence: ["MIT", "GPL-3.0-or-later"]
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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: VCF file (optionally GZIPPED)
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pattern: "*.{vcf,vcf.gz}"
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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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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- csi:
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type: file
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description: Default VCF file index file
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pattern: "*.csi"
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- tbi:
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type: file
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description: Alternative VCF file index file for larger files (activated with -t parameter)
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pattern: "*.tbi"
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authors:
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- "@jfy133"
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