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59 lines
1.5 KiB
YAML
59 lines
1.5 KiB
YAML
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name: biscuit_epiread
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description: |
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Summarizes read-level methylation (and optionally SNV) information from a
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Biscuit BAM file in a standard-compliant BED format.
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keywords:
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- biscuit
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- DNA methylation
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- WGBS
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- scWGBS
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- bisulfite sequencing
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- aligner
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- bam
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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/epiread_format/
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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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- bam:
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type: file
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description: Biscuit BAM file
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- bai:
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type: file
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description: BAM index
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- snp_bed:
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type: file
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description: BED file containing SNP information (optional)
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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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- epiread_bed:
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type: file
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description: Gzipped BED file with methylation (and optionally SNV) information
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pattern: "*.{epiread.bed.gz}"
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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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- "@njspix"
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