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2ad98162f3
* Draft rmarkdown module * stub jupyter notebook module * Create yaml file with params * Update meta.yml for rmarkdown module * Add comment on YAML * Update notebooks module, clean up parametrize.nf * Two separate channels for parameters and input files * Fix Rmd render script * Add tests for rmarkdown * Fix tests for rmarkdown module * Update checksums * Fix tests for jupyter * Test without Grab() * Update software versions * update rmarkdown dependencies * Draft for multiple versions * Fix indent of script * Fix indent in rmarkdown script * Emit version.syml * Update modules/rmarkdown/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Rename rmarkdown to rmarkdownnotebook * Add rmarkdown mulled biocontainer * Write sessionInfo to separate log file * Update rmarkdownnotebook * Sessioninfo does not have a stable md5sum * Update jupyternotebook * Update meta * Add jupyternotebook biocontainers * Handle Groovy Gstrings in parameterize * Update to versions.yml * Update functions.nf * Fix versions yaml * Fix EC lint * Update modules/rmarkdownnotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/jupyternotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Use official test data * Harshilify * Make parameters channel clearer * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
73 lines
2.1 KiB
YAML
73 lines
2.1 KiB
YAML
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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