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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
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: methyldackel_extract
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description: Extracts per-base methylation metrics from alignments
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keywords:
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- consensus
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- bedGraph
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- bam
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- cram
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tools:
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- methyldackel:
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description: |
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A (mostly) universal methylation extractor
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for BS-seq experiments.
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homepage: https://github.com/brentp/bwa-meth
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documentation: https://github.com/brentp/bwa-meth
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arxiv: arXiv:1401.1129
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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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- fasta:
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type: file
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description: Input genome fasta file
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pattern: "*.{fasta,fa}"
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- fai:
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type: file
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description: FASTA index file
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pattern: "*.{fai}"
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- bam:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- bai:
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type: file
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description: BAM/CRAM index file
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pattern: "*.{bai,crai}"
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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: bedGraph file containing per-base methylation metrics
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pattern: "*.{bedGraph}"
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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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