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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>
64 lines
1.8 KiB
YAML
64 lines
1.8 KiB
YAML
name: plink2_extract
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description: Subset plink pfiles with a text file of variant identifiers
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keywords:
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- plink2
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- extract
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tools:
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- plink2:
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description: |
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Whole genome association analysis toolset, designed to perform a range
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of basic, large-scale analyses in a computationally efficient manner
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homepage: http://www.cog-genomics.org/plink/2.0/
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documentation: http://www.cog-genomics.org/plink/2.0/general_usage
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tool_dev_url: None
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doi: "10.1186/s13742-015-0047-8"
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licence: ["GPL v3"]
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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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- pgen:
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type: file
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description: PLINK 2 binary genotype table
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pattern: "*.{pgen}"
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- psam:
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type: file
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description: PLINK 2 sample information file
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pattern: "*.{psam}"
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- pvar:
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type: file
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description: PLINK 2 variant information file
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pattern: "*.{pvar}"
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- variants:
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type: file
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description: A text file containing variant identifiers to keep (one per line)
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pattern: "*.{keep}"
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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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- 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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- extract_pgen:
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type: file
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description: PLINK 2 binary genotype table, containing extracted variants
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pattern: "*.{pgen}"
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- extract_psam:
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type: file
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description: PLINK 2 sample information file associated with the extracted data
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pattern: "*.{psam}"
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- extract_pvar:
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type: file
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description: PLINK 2 variant information file, containing extracted variants
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pattern: "*.{pvar.zst}"
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authors:
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- "@nebfield"
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