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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
54 lines
2 KiB
YAML
54 lines
2 KiB
YAML
name: gatk4_calculatecontamination
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description: |
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Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
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keywords:
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- gatk4
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- calculatecontamination
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- cross-samplecontamination
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- getpileupsummaries
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- filtermutectcalls
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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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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' ]
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- pileup:
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type: file
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description: File containing the pileups summary table of a tumor sample to be used to calculate contamination.
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pattern: "*.pileups.table"
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- matched:
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type: file
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description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.
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pattern: "*.pileups.table"
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- segmentout:
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type: boolean
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description: specifies whether to output the segmentation table.
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output:
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- contamination:
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type: file
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description: File containing the contamination table.
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pattern: "*.contamination.table"
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- segmentation:
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type: file
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description: optional output table containing segmentation of tumor minor allele fractions.
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pattern: "*.segmentation.table"
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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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authors:
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- "@GCJMackenzie"
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