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66 lines
2 KiB
YAML
66 lines
2 KiB
YAML
name: bismark_methylationextractor
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description: Extracts methylation information for individual cytosines from alignments.
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keywords:
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- bismark
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- consensus
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- map
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- bam
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- bedGraph
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tools:
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- bismark:
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description: |
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Bismark is a tool to map bisulfite treated sequencing reads
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and perform methylation calling in a quick and easy-to-use fashion.
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homepage: https://github.com/FelixKrueger/Bismark
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documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
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doi: 10.1093/bioinformatics/btr167
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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 containing read alignments
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pattern: "*.{bam}"
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- index:
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type: dir
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description: Bismark genome index directory
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pattern: "BismarkIndex"
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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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- bedgraph:
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type: file
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description: Bismark output file containing coverage and methylation metrics
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pattern: "*.{bedGraph.gz}"
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- methylation_calls:
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type: file
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description: Bismark output file containing strand-specific methylation calls
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pattern: "*.{txt.gz}"
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- coverage:
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type: file
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description: Bismark output file containing coverage metrics
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pattern: "*.{cov.gz}"
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- report:
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type: file
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description: Bismark splitting reports
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pattern: "*_{splitting_report.txt}"
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- mbias:
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type: file
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description: Text file containing methylation bias information
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pattern: "*.{M-bias.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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- "@phue"
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