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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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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