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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>
27 lines
932 B
YAML
27 lines
932 B
YAML
- name: rmarkdownnotebook test_rmarkdown
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command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown -c tests/config/nextflow.config
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tags:
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- rmarkdownnotebook
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files:
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- path: output/rmarkdownnotebook/session_info.log
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contains:
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- R version 4.1.0
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- yaml_2.2.1
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- path: output/rmarkdownnotebook/test_rmd.html
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contains:
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- "n_iter = 10"
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- name: rmarkdownnotebook test_rmarkdown_parametrize
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command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown_parametrize -c tests/config/nextflow.config
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tags:
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- rmarkdownnotebook
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files:
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- path: output/rmarkdownnotebook/artifacts/artifact.txt
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md5sum: b10a8db164e0754105b7a99be72e3fe5
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- path: output/rmarkdownnotebook/session_info.log
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contains:
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- R version 4.1.0
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- yaml_2.2.1
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- path: output/rmarkdownnotebook/test_rmd.html
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contains:
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- "n_iter = 12"
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