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71 lines
2.3 KiB
YAML
71 lines
2.3 KiB
YAML
name: biscuit_pileup
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description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
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keywords:
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- bisulfite
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- DNA methylation
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- pileup
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- variant calling
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- WGBS
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- scWGBS
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- bam
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- vcf
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tools:
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- biscuit:
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description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
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homepage: https://huishenlab.github.io/biscuit/
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documentation: https://huishenlab.github.io/biscuit/docs/pileup.html
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tool_dev_url: https://github.com/huishenlab/biscuit
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doi: ""
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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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- normal_bams:
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type: file(s)
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description: |
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BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
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("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
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tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
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pattern: "*.{bam}"
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- normal_bais:
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type: file(s)
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description: BAM index file or files corresponding to the provided normal_bams
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pattern: "*.{bai}"
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- tumor_bam:
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type: file(s)
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description: |
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Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
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their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
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tumor BAM file is provided, exactly one normal BAM must be provided.
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pattern: "*.{bam}"
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- tumor_bai:
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type: file(s)
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description: Optional. BAM index file corresponding to provided tumor_bam
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pattern: "*.{bai}"
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- index:
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type: dir
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description: Biscuit genome index directory (generated with 'biscuit index')
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pattern: "BiscuitIndex"
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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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- vcf:
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type: file
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description: vcf file with methylation information
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pattern: "*.{vcf.gz}"
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authors:
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- "@njspix"
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