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83 lines
3.2 KiB
Text
83 lines
3.2 KiB
Text
include { dump_params_yml; indent_code_block } from "./parametrize"
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process JUPYTERNOTEBOOK {
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tag "$meta.id"
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label 'process_low'
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//NB: You likely want to override this with a container containing all required
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//dependencies for your analysis. The container at least needs to contain the
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//ipykernel, jupytext, papermill and nbconvert Python packages.
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conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
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'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
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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 args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize
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def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
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def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
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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 (parametrize) {
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nb_params = [:]
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if (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 (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 ${prefix}.html
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cat <<-END_VERSIONS > versions.yml
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"${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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