mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
86 lines
3.3 KiB
Text
86 lines
3.3 KiB
Text
include { dump_params_yml; indent_code_block } from "./parametrize"
|
|
|
|
process JUPYTERNOTEBOOK {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
//NB: You likely want to override this with a container containing all required
|
|
//dependencies for your analysis. The container at least needs to contain the
|
|
//ipykernel, jupytext, papermill and nbconvert Python packages.
|
|
conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
|
|
'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(notebook)
|
|
val parameters
|
|
path input_files
|
|
|
|
output:
|
|
tuple val(meta), path("*.html"), emit: report
|
|
tuple val(meta), path("artifacts/"), emit: artifacts, optional: true
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize
|
|
def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
|
|
def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
|
|
|
|
// 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 (parametrize) {
|
|
nb_params = [:]
|
|
if (implicit_params) {
|
|
nb_params["cpus"] = task.cpus
|
|
nb_params["artifact_dir"] = "artifacts"
|
|
nb_params["input_dir"] = "./"
|
|
}
|
|
if (meta_params) {
|
|
nb_params["meta"] = meta
|
|
}
|
|
nb_params += parameters
|
|
params_cmd = dump_params_yml(nb_params)
|
|
render_cmd = "papermill -f .params.yml"
|
|
} else {
|
|
render_cmd = "papermill"
|
|
}
|
|
|
|
"""
|
|
set -o pipefail
|
|
|
|
# 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"
|
|
export NUMBA_NUM_THREADS="$task.cpus"
|
|
|
|
# Convert notebook to ipynb using jupytext, execute using papermill, convert using nbconvert
|
|
jupytext --to notebook --output - --set-kernel - ${notebook} \\
|
|
| ${render_cmd} \\
|
|
| jupyter nbconvert --stdin --to html --output ${prefix}.html
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
jupytext: \$(jupytext --version)
|
|
ipykernel: \$(python -c "import ipykernel; print(ipykernel.__version__)")
|
|
nbconvert: \$(jupyter nbconvert --version)
|
|
papermill: \$(papermill --version | cut -f1 -d' ')
|
|
END_VERSIONS
|
|
"""
|
|
}
|