nf-core_modules/tests/modules/rmarkdownnotebook/test.yml

- name: rmarkdownnotebook test_rmarkdown
  command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown -c tests/config/nextflow.config
  tags:
    - rmarkdownnotebook
  files:
    - path: output/rmarkdownnotebook/session_info.log
      contains:
        - R version 4.1.0
        - yaml_2.2.1
    - path: output/rmarkdownnotebook/test_rmd.html
      contains:
        - "n_iter = 10"

- name: rmarkdownnotebook test_rmarkdown_parametrize
  command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown_parametrize -c tests/config/nextflow.config
  tags:
    - rmarkdownnotebook
  files:
    - path: output/rmarkdownnotebook/artifacts/artifact.txt
      md5sum: b10a8db164e0754105b7a99be72e3fe5
    - path: output/rmarkdownnotebook/session_info.log
      contains:
        - R version 4.1.0
        - yaml_2.2.1
    - path: output/rmarkdownnotebook/test_rmd.html
      contains:
        - "n_iter = 12"
Notebook modules (#617) * 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> 2021-10-24 18:51:56 +00:00			`- name: rmarkdownnotebook test_rmarkdown`
			`command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown -c tests/config/nextflow.config`
			`tags:`
			`- rmarkdownnotebook`
			`files:`
			`- path: output/rmarkdownnotebook/session_info.log`
			`contains:`
			`- R version 4.1.0`
			`- yaml_2.2.1`
			`- path: output/rmarkdownnotebook/test_rmd.html`
			`contains:`
			`- "n_iter = 10"`

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