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https://github.com/MillironX/nf-core_modules.git
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74 lines
2.1 KiB
YAML
74 lines
2.1 KiB
YAML
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name: rmarkdownnotebook
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description: Render an rmarkdown notebook. Supports parametrization.
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keywords:
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- R
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- notebook
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- reports
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tools:
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- rmarkdown:
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description: Dynamic Documents for R
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homepage: https://rmarkdown.rstudio.com/
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documentation: https://rmarkdown.rstudio.com/lesson-1.html
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tool_dev_url: https://github.com/rstudio/rmarkdown
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doi: ""
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licence: GPL-3
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params:
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- parametrize:
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type: boolean
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description: If true, parametrize the notebook
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- implicit_params:
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type: boolean
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description: |
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If true (default), include the implicit params
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* `input_dir`, which points to the directory containing the files added via `input_files`,
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* `artifact_dir`, which points to the directory where the notebook should place output files, and
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* `cpus`, which contains the value of ${task.cpus}
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- meta_params:
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type: boolean
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description: |
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If true, include a parameter `meta` which contains the information specified
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via the `meta` input channel.
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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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- notebook:
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type: file
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description: Rmarkdown file
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pattern: "*.{Rmd}"
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- parameters:
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type: map
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description: |
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Groovy map with notebook parameters which will be passed to
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rmarkdown to generate parametrized reports.
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- input_files:
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type: path
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description: One or multiple files serving as input data for the notebook.
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pattern: "*"
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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: HTML report generated from Rmarkdown
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pattern: "*.html"
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- session_info:
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type: file
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description: dump of R SessionInfo
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@grst"
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