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https://github.com/MillironX/nf-core_modules.git
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52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
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name: biscuit_qc
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description: Perform basic quality control on a BAM file generated with Biscuit
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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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- index
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- BAM
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- quality control
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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/subcommand_help.html#biscuit-qc
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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: BAM file produced using Biscuit
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output:
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- biscuit_qc_reports:
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type: file
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description: |
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Summary files containing the following information:
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- CpG retention by position in read
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- CpH retention by position in read
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- Read duplication statistics
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- Insert size distribution
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- Distribution of mapping qualities
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- Proportion of reads mapping to each strand
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- Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
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pattern: "*.txt"
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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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