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63 lines
2.2 KiB
YAML
63 lines
2.2 KiB
YAML
name: bedtools_complement
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description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
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keywords:
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- bed
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- complement
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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/complement.html
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params:
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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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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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: Input BED file
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pattern: "*.{bed}"
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- sizes:
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type: file
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description: File which defines the chromosome lengths for a given genome
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pattern: "*.{sizes}"
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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: Bed file with all genomic intervals that are not covered by at least one record from the input file.
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pattern: "*.{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:
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- "@Emiller88"
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- "@sruthipsuresh"
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- "@drpatelh"
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