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75 lines
2.2 KiB
YAML
75 lines
2.2 KiB
YAML
name: bedtools_slop
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description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
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keywords:
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- bed
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- slopBed
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tools:
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- bedtools:
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description: |
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A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
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documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
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params:
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- l:
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type: integer
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description: The number of base pairs to subtract from the start coordinate
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- r:
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type: integer
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description: The number of base pairs to add to the end coordinate
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- b:
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type: integer
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description: Increases the entry by the same number base pairs in each direction
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- pct:
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type: boolean
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description: |
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Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.
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- header:
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type: boolean
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description: |
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Print the header from the input file prior to results.
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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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: List of bed files
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pattern: "*.{bed}"
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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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- bed:
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type: file
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description: Edited bed file
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pattern: "*.{slop.bed}"
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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: "*.{version.txt}"
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authors: -"@Emiller88"
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-"@sruthipsuresh"
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