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55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: "haplocheck"
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description: |
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Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing
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the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides
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users a graphical report to investigate the contamination further. Internally, it uses the
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Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
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keywords:
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- mitochondrial
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- mtDNA
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- contamination
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tools:
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- "haplocheck":
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description: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content."
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homepage: "https://github.com/genepi/haplocheck"
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documentation: "https://github.com/genepi/haplocheck"
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tool_dev_url: "https://github.com/genepi/haplocheck"
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doi: 10.1101/gr.256545.119
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licence: "['MIT']"
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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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- vcf:
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type: file
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description: VCF file
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pattern: "*.{vcf.gz}"
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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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- txt:
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type: file
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description: Raw report in txt format
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pattern: "*.{txt}"
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- html:
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type: file
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description: Haplocheck HTML report
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pattern: "*.{html}"
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authors:
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- "@lmtani"
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