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meta.yml
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meta.yml
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name: gatk4_splitncigarreads
description: Splits reads that contain Ns in their cigar string
keywords:
- vcf
- merge
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- bam:
type: list
description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}"
- bai:
type: list
description: BAI/SAI/CRAI index file (optional)
pattern: "*.{bai,sai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- bam:
type: file
description: Output file with split reads (BAM/SAM/CRAM)
pattern: "*.{bam,sam,cram}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@kevinmenden"