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55 lines
1.8 KiB
YAML
55 lines
1.8 KiB
YAML
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name: bedtools_getfasta
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description: extract sequences in a FASTA file based on intervals defined in a feature file.
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keywords:
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- bed
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- fasta
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- getfasta
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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/intersect.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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- bed:
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type: file
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description: Bed feature file
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pattern: "*.{bed}"
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- fasta:
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type: file
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description: Input fasta file
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pattern: "*.{fa,fasta}"
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output:
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- fasta:
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type: file
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description: Output fasta file with extracted sequences
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pattern: "*.{fa}"
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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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- "@joseespinosa"
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- "@drpatelh"
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