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>unifiedgenotyper
Gregor Sturm
3 years ago
committed by
GitHub
parent
0a5ddd0ad0
commit
2ad98162f3
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -0,0 +1,92 @@
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// Import generic module functions
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include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
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include { dump_params_yml; indent_code_block } from "./parametrize"
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params.options = [:]
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options = initOptions(params.options)
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params.parametrize = true
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params.implicit_params = true
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params.meta_params = true
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process JUPYTERNOTEBOOK {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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//NB: You likely want to override this with a container containing all required
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//dependencies for your analysis. The container at least needs to contain the
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//ipykernel, jupytext, papermill and nbconvert Python packages.
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conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0"
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}
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input:
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tuple val(meta), path(notebook)
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val parameters
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path input_files
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output:
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tuple val(meta), path("*.html"), emit: report
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tuple val(meta), path("artifacts/"), emit: artifacts, optional: true
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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// Dump parameters to yaml file.
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// Using a yaml file over using the CLI params because
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// * no issue with escaping
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// * allows to pass nested maps instead of just single values
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def params_cmd = ""
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def render_cmd = ""
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if (params.parametrize) {
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nb_params = [:]
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if (params.implicit_params) {
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nb_params["cpus"] = task.cpus
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nb_params["artifact_dir"] = "artifacts"
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nb_params["input_dir"] = "./"
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}
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if (params.meta_params) {
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nb_params["meta"] = meta
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}
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nb_params += parameters
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params_cmd = dump_params_yml(nb_params)
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render_cmd = "papermill -f .params.yml"
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} else {
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render_cmd = "papermill"
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}
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"""
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set -o pipefail
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# Dump .params.yml heredoc (section will be empty if parametrization is disabled)
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${indent_code_block(params_cmd, 4)}
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# Create output directory
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mkdir artifacts
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# Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
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export MKL_NUM_THREADS="${task.cpus}"
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export OPENBLAS_NUM_THREADS="${task.cpus}"
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export OMP_NUM_THREADS="${task.cpus}"
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export NUMBA_NUM_THREADS="${task.cpus}"
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# Convert notebook to ipynb using jupytext, execute using papermill, convert using nbconvert
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jupytext --to notebook --output - --set-kernel - ${notebook} \\
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| ${render_cmd} \\
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| jupyter nbconvert --stdin --to html --output ${prefix}.html
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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jupytext: \$(jupytext --version)
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ipykernel: \$(python -c "import ipykernel; print(ipykernel.__version__)")
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nbconvert: \$(jupyter nbconvert --version)
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papermill: \$(papermill --version | cut -f1 -d' ')
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END_VERSIONS
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"""
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}
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name: jupyternotebook
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description: |
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Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization
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through papermill.
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keywords:
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- Python
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- Jupyter
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- jupytext
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- papermill
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- notebook
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- reports
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tools:
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- jupytext:
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description: Jupyter notebooks as plain text scripts or markdown documents
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homepage: https://github.com/mwouts/jupytext/
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documentation: https://jupyter.org/documentation
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tool_dev_url: https://github.com/mwouts/jupytext/
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licence: "MIT"
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- papermill:
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description: Parameterize, execute, and analyze notebooks
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homepage: https://github.com/nteract/papermill
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documentation: http://papermill.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/nteract/papermill
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licence: "BSD 3-clause"
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- nbconvert:
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description: Parameterize, execute, and analyze notebooks
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homepage: https://nbconvert.readthedocs.io/en/latest/
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documentation: https://nbconvert.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/jupyter/nbconvert
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licence: "BSD 3-clause"
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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: Jupyter notebook or jupytext representation thereof
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pattern: "*.{ipynb,py,md,Rmd,myst}"
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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
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to papermill in order to create 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 Jupyter notebook
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pattern: "*.html"
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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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import org.yaml.snakeyaml.Yaml
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import org.yaml.snakeyaml.representer.Representer
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import org.yaml.snakeyaml.DumperOptions
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/**
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* Multiline code blocks need to have the same indentation level
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* as the `script:` section. This function re-indents code to the specified level.
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*/
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def indent_code_block(code, n_spaces) {
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def indent_str = " ".multiply(n_spaces)
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return code.stripIndent().split("\n").join("\n" + indent_str)
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}
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/**
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* Create a config YAML file from a groovy map
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*
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* @params task The process' `task` variable
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* @returns a line to be inserted in the bash script.
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*/
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def dump_params_yml(params) {
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DumperOptions options = new DumperOptions();
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options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK);
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// Properly handle Groovy GStrings
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// see https://stackoverflow.com/a/35108062/2340703
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def representer = new Representer() {{
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this.multiRepresenters.put(GString, this.representers.get(String))
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}}
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def yaml = new Yaml(representer, options)
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def yaml_str = yaml.dump(params)
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// Writing the .params.yml file directly as follows does not work.
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// It only works in 'exec:', but not if there is a `script:` section:
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// task.workDir.resolve('.params.yml').text = yaml_str
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// Therefore, we inject it into the bash script:
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return """\
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cat <<"END_PARAMS_SECTION" > ./.params.yml
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${indent_code_block(yaml_str, 8)}
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END_PARAMS_SECTION
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"""
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}
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@ -0,0 +1,78 @@
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -0,0 +1,97 @@
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// Import generic module functions
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include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
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include { dump_params_yml; indent_code_block } from "./parametrize"
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params.options = [:]
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options = initOptions(params.options)
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params.parametrize = true
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params.implicit_params = true
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params.meta_params = true
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process RMARKDOWNNOTEBOOK {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
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|
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//NB: You likely want to override this with a container containing all required
|
||||
//dependencies for your analysis. The container at least needs to contain the
|
||||
//yaml and rmarkdown R packages.
|
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conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
|
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
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container "https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0"
|
||||
} else {
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container "quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0"
|
||||
}
|
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|
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input:
|
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tuple val(meta), path(notebook)
|
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val parameters
|
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path input_files
|
||||
|
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output:
|
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tuple val(meta), path("*.html") , emit: report
|
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tuple val(meta), path ("artifacts/*") , emit: artifacts, optional: true
|
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tuple val(meta), path ("session_info.log"), emit: session_info
|
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path "versions.yml" , emit: versions
|
||||
|
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script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
|
||||
// Dump parameters to yaml file.
|
||||
// Using a yaml file over using the CLI params because
|
||||
// * no issue with escaping
|
||||
// * allows to pass nested maps instead of just single values
|
||||
def params_cmd = ""
|
||||
def render_cmd = ""
|
||||
if (params.parametrize) {
|
||||
nb_params = [:]
|
||||
if (params.implicit_params) {
|
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nb_params["cpus"] = task.cpus
|
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nb_params["artifact_dir"] = "artifacts"
|
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nb_params["input_dir"] = "./"
|
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}
|
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if (params.meta_params) {
|
||||
nb_params["meta"] = meta
|
||||
}
|
||||
nb_params += parameters
|
||||
params_cmd = dump_params_yml(nb_params)
|
||||
render_cmd = """\
|
||||
params = yaml::read_yaml('.params.yml')
|
||||
rmarkdown::render('${prefix}.Rmd', params=params, envir=new.env())
|
||||
"""
|
||||
} else {
|
||||
render_cmd = "rmarkdown::render('${prefix}.Rmd')"
|
||||
}
|
||||
|
||||
"""
|
||||
# Dump .params.yml heredoc (section will be empty if parametrization is disabled)
|
||||
${indent_code_block(params_cmd, 4)}
|
||||
|
||||
# Create output directory
|
||||
mkdir artifacts
|
||||
|
||||
# Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
|
||||
export MKL_NUM_THREADS="${task.cpus}"
|
||||
export OPENBLAS_NUM_THREADS="${task.cpus}"
|
||||
export OMP_NUM_THREADS="${task.cpus}"
|
||||
|
||||
# Work around https://github.com/rstudio/rmarkdown/issues/1508
|
||||
# If the symbolic link is not replaced by a physical file
|
||||
# output- and temporary files will be written to the original directory.
|
||||
mv "${notebook}" "${notebook}.orig"
|
||||
cp -L "${notebook}.orig" "${prefix}.Rmd"
|
||||
|
||||
# Render notebook
|
||||
Rscript - <<EOF
|
||||
${indent_code_block(render_cmd, 8)}
|
||||
writeLines(capture.output(sessionInfo()), "session_info.log")
|
||||
EOF
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
rmarkdown: \$(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,73 @@
|
||||
name: rmarkdownnotebook
|
||||
description: Render an rmarkdown notebook. Supports parametrization.
|
||||
keywords:
|
||||
- R
|
||||
- notebook
|
||||
- reports
|
||||
tools:
|
||||
- rmarkdown:
|
||||
description: Dynamic Documents for R
|
||||
homepage: https://rmarkdown.rstudio.com/
|
||||
documentation: https://rmarkdown.rstudio.com/lesson-1.html
|
||||
tool_dev_url: https://github.com/rstudio/rmarkdown
|
||||
doi: ""
|
||||
licence: GPL-3
|
||||
|
||||
params:
|
||||
- parametrize:
|
||||
type: boolean
|
||||
description: If true, parametrize the notebook
|
||||
- implicit_params:
|
||||
type: boolean
|
||||
description: |
|
||||
If true (default), include the implicit params
|
||||
* `input_dir`, which points to the directory containing the files added via `input_files`,
|
||||
* `artifact_dir`, which points to the directory where the notebook should place output files, and
|
||||
* `cpus`, which contains the value of ${task.cpus}
|
||||
- meta_params:
|
||||
type: boolean
|
||||
description: |
|
||||
If true, include a parameter `meta` which contains the information specified
|
||||
via the `meta` input channel.
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- notebook:
|
||||
type: file
|
||||
description: Rmarkdown file
|
||||
pattern: "*.{Rmd}"
|
||||
- parameters:
|
||||
type: map
|
||||
description: |
|
||||
Groovy map with notebook parameters which will be passed to
|
||||
rmarkdown to generate parametrized reports.
|
||||
- input_files:
|
||||
type: path
|
||||
description: One or multiple files serving as input data for the notebook.
|
||||
pattern: "*"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: HTML report generated from Rmarkdown
|
||||
pattern: "*.html"
|
||||
- session_info:
|
||||
type: file
|
||||
description: dump of R SessionInfo
|
||||
pattern: "*.log"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@grst"
|
||||
@ -0,0 +1,36 @@
|
||||
import org.yaml.snakeyaml.Yaml
|
||||
import org.yaml.snakeyaml.DumperOptions
|
||||
|
||||
|
||||
/**
|
||||
* Multiline code blocks need to have the same indentation level
|
||||
* as the `script:` section. This function re-indents code to the specified level.
|
||||
*/
|
||||
def indent_code_block(code, n_spaces) {
|
||||
def indent_str = " ".multiply(n_spaces)
|
||||
return code.stripIndent().split("\n").join("\n" + indent_str)
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a config YAML file from a groovy map
|
||||
*
|
||||
* @params task The process' `task` variable
|
||||
* @returns a line to be inserted in the bash script.
|
||||
*/
|
||||
def dump_params_yml(params) {
|
||||
DumperOptions options = new DumperOptions();
|
||||
options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK);
|
||||
def yaml = new Yaml(options)
|
||||
def yaml_str = yaml.dump(params)
|
||||
|
||||
// Writing the .params.yml file directly as follows does not work.
|
||||
// It only works in 'exec:', but not if there is a `script:` section:
|
||||
// task.workDir.resolve('.params.yml').text = yaml_str
|
||||
|
||||
// Therefore, we inject it into the bash script:
|
||||
return """\
|
||||
cat <<"END_PARAMS_SECTION" > ./.params.yml
|
||||
${indent_code_block(yaml_str, 8)}
|
||||
END_PARAMS_SECTION
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,49 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf' addParams(
|
||||
parametrize: false, options: [:]
|
||||
)
|
||||
include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf' addParams(
|
||||
options: [:]
|
||||
)
|
||||
include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf' addParams(
|
||||
options: [:]
|
||||
)
|
||||
|
||||
workflow test_jupyternotebook {
|
||||
|
||||
input = [ [ id:'test_jupyter' ], // meta map
|
||||
file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
|
||||
|
||||
JUPYTERNOTEBOOK ( input, [:], [])
|
||||
|
||||
}
|
||||
|
||||
workflow test_jupyternotebook_parametrize {
|
||||
|
||||
input = [ [ id:'test_jupyter' ], // meta map
|
||||
file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
|
||||
|
||||
JUPYTERNOTEBOOK_PARAMETRIZE(
|
||||
input,
|
||||
[input_filename: "hello.txt", n_iter: 12],
|
||||
file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
workflow test_jupyternotebook_parametrize_ipynb {
|
||||
|
||||
input = [ [ id:'test_jupyter' ], // meta map
|
||||
file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) ]
|
||||
|
||||
JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB(
|
||||
input,
|
||||
[input_filename: "hello.txt", n_iter: 12],
|
||||
file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
@ -0,0 +1,30 @@
|
||||
- name: jupyternotebook test_jupyternotebook
|
||||
command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook -c tests/config/nextflow.config
|
||||
tags:
|
||||
- jupyternotebook
|
||||
files:
|
||||
- path: output/jupyternotebook/test_jupyter.html
|
||||
contains:
|
||||
- "n_iter = 10"
|
||||
|
||||
- name: jupyternotebook test_jupyternotebook_parametrize
|
||||
command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize -c tests/config/nextflow.config
|
||||
tags:
|
||||
- jupyternotebook
|
||||
files:
|
||||
- path: output/jupyternotebook/artifacts/artifact.txt
|
||||
md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
|
||||
- path: output/jupyternotebook/test_jupyter.html
|
||||
contains:
|
||||
- "n_iter = 12"
|
||||
|
||||
- name: jupyternotebook test_jupyternotebook_parametrize_ipynb
|
||||
command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize_ipynb -c tests/config/nextflow.config
|
||||
tags:
|
||||
- jupyternotebook
|
||||
files:
|
||||
- path: output/jupyternotebook/artifacts/artifact.txt
|
||||
md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
|
||||
- path: output/jupyternotebook/test_jupyter.html
|
||||
contains:
|
||||
- "n_iter = 12"
|
||||
@ -0,0 +1,33 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { RMARKDOWNNOTEBOOK } from '../../../modules/rmarkdownnotebook/main.nf' addParams(
|
||||
parametrize: false, options: [:]
|
||||
)
|
||||
include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/rmarkdownnotebook/main.nf' addParams(
|
||||
options: [:]
|
||||
)
|
||||
|
||||
workflow test_rmarkdown {
|
||||
|
||||
input = [ [ id:'test_rmd' ], // meta map
|
||||
file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
|
||||
|
||||
RMARKDOWNNOTEBOOK ( input, [:], [])
|
||||
|
||||
}
|
||||
|
||||
workflow test_rmarkdown_parametrize {
|
||||
|
||||
input = [ [ id:'test_rmd' ], // meta map
|
||||
file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
|
||||
|
||||
RMARKDOWNNOTEBOOK_PARAMETRIZE(
|
||||
input,
|
||||
[input_filename: "hello.txt", n_iter: 12],
|
||||
file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
@ -0,0 +1,27 @@
|
||||
- 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"
|
||||
Loading…
Reference in New Issue