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* 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>
49 lines
1.4 KiB
Text
49 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf' addParams(
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parametrize: false, options: [:]
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)
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include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf' addParams(
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options: [:]
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)
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include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf' addParams(
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options: [:]
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)
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workflow test_jupyternotebook {
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input = [ [ id:'test_jupyter' ], // meta map
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file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
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JUPYTERNOTEBOOK ( input, [:], [])
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}
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workflow test_jupyternotebook_parametrize {
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input = [ [ id:'test_jupyter' ], // meta map
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file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
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JUPYTERNOTEBOOK_PARAMETRIZE(
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input,
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[input_filename: "hello.txt", n_iter: 12],
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file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
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)
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}
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workflow test_jupyternotebook_parametrize_ipynb {
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input = [ [ id:'test_jupyter' ], // meta map
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file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) ]
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JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB(
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input,
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[input_filename: "hello.txt", n_iter: 12],
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file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
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)
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}
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