2021-02-19 13:59:29 +00:00
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name: gatk4_splitncigarreads
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description: Splits reads that contain Ns in their cigar string
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keywords:
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- vcf
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- merge
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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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']
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- bam:
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type: list
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description: BAM/SAM/CRAM file containing reads
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pattern: "*.{bam,sam,cram}"
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- fasta:
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2021-02-22 12:31:54 +00:00
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type: tuple of files
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description: |
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Tuple of fasta file (first), sequence dict (second) and fasta index (third)
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pattern: ["*.fasta", "*.dict", "*.fai"]
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2021-02-19 13:59:29 +00:00
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output:
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- bam:
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type: file
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description: Output file with split reads (BAM/SAM/CRAM)
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pattern: "*.{bam,sam,cram}"
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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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- "@kevinmenden"
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