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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
51 lines
1.5 KiB
YAML
51 lines
1.5 KiB
YAML
name: bismark_deduplicate
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description: |
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Removes alignments to the same position in the genome
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from the Bismark mapping output.
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keywords:
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- bismark
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- 3-letter genome
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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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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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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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- bam:
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type: file
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description: Deduplicated output BAM file containing read alignments
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pattern: "*.{deduplicated.bam}"
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- 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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- 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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