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73 lines
2.2 KiB
YAML
73 lines
2.2 KiB
YAML
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name: "gatk4_collectreadcounts"
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description: Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.
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keywords:
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- bam
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- cram
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- CollectReadCounts
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- gatk
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- gatk4
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tools:
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- gatk4:
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description:
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Genome Analysis Toolkit (GATK4). 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/articles/360037593911-CombineGVCFs
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tool_dev_url: https://github.com/broadinstitute/gatk
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ["Apache-2.0"]
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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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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- intervals:
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type: file
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description: A file containing the specified intervals
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pattern: "*.{bed,intervals}"
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- fasta:
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type: file
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description: Optional - Reference FASTA
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pattern: "*.{fasta,fa}"
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- fai:
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type: file
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description: Optional - Index of the reference FASTA file
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pattern: "*.fai"
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- dict:
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type: file
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description: Optional - Sequence dictionary of the reference FASTA file
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pattern: "*.dict"
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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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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- hdf5:
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type: file
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description: The read counts in hdf5 format
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pattern: "*.hdf5"
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- tsv:
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type: file
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description: The read counts in TSV format
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pattern: "*.tsv"
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authors:
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- "@nvnieuwk"
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