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79 lines
2.3 KiB
YAML
79 lines
2.3 KiB
YAML
name: methyldackel_mbias
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description: Generates methylation bias plots 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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- methylation bias
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- mbias
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- qc
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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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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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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- txt:
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type: file
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description: Text file containing methylation bias
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pattern: "*.{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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