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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>
51 lines
1.3 KiB
YAML
51 lines
1.3 KiB
YAML
name: scoary
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description: Use pangenome outputs for GWAS
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keywords:
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- gwas
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- pangenome
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- prokaryote
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tools:
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- scoary:
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description: Microbial pan-GWAS using the output from Roary
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homepage: https://github.com/AdmiralenOla/Scoary
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documentation: https://github.com/AdmiralenOla/Scoary
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tool_dev_url: https://github.com/AdmiralenOla/Scoary
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doi: "10.1186/s13059-016-1108-8"
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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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- genes:
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type: file
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description: A presence/absence matrix of genes in the pan-genome
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pattern: "*.csv"
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- traits:
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type: file
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description: A CSV file containing trait information per-sample
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pattern: "*.csv"
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- tree:
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type: file
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description: A Newick formtted tree for phylogenetic analyses
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pattern: "*.{dnd,nwk,treefile}"
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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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- csv:
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type: file
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description: Gene associations in a CSV file per trait
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pattern: "*.csv"
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authors:
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- "@rpetit3"
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