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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>
62 lines
1.6 KiB
YAML
62 lines
1.6 KiB
YAML
name: plink_extract
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description: Subset plink bfiles with a text file of variant identifiers
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keywords:
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- extract
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- plink
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tools:
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- plink:
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description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
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homepage: None
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documentation: None
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tool_dev_url: None
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doi: ""
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licence: ["GPL"]
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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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- bed:
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type: file
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description: PLINK binary biallelic genotype table
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pattern: "*.{bed}"
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- bim:
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type: file
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description: PLINK extended MAP file
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pattern: "*.{bim}"
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- fam:
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type: file
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description: PLINK sample information file
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pattern: "*.{fam}"
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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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- bed:
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type: file
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description: PLINK binary biallelic genotype table
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pattern: "*.{bed}"
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- bim:
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type: file
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description: PLINK extended MAP file
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pattern: "*.{bim}"
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- fam:
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type: file
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description: PLINK sample information file
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pattern: "*.{fam}"
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authors:
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- "@nebfield"
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