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58 lines
1.8 KiB
YAML
58 lines
1.8 KiB
YAML
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name: bismark_genome_preparation
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description: |
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Converts a specified reference genome into two different bisulfite
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converted versions and indexes them for alignments.
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keywords:
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- bismark
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- 3-letter genome
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- index
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- fasta
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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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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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- 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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- 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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- 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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