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f9ce8664ba
* add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: bismark_report
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description: Collects bismark alignment reports
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keywords:
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- bismark
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- qc
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- report
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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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- align_report:
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type: file
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description: Bismark alignment reports
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pattern: "*{report.txt}"
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- splitting_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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- dedup_report:
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type: file
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description: Bismark deduplication reports
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pattern: "*.{deduplication_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: "*.{txt}"
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- fasta:
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type: file
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description: Input genome fasta file
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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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- report:
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type: file
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description: Bismark reports
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pattern: "*.{html,txt}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@phue"
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