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88 lines
3.4 KiB
Text
88 lines
3.4 KiB
Text
include { dump_params_yml; indent_code_block } from "./parametrize"
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process RMARKDOWNNOTEBOOK {
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tag "$meta.id"
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label 'process_low'
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//NB: You likely want to override this with a container containing all required
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//dependencies for your analysis. The container at least needs to contain the
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//yaml and rmarkdown R packages.
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conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
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'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
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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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tuple val(meta), path ("session_info.log"), emit: session_info
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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 = """\
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params = yaml::read_yaml('.params.yml')
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rmarkdown::render('${prefix}.Rmd', params=params, envir=new.env())
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"""
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} else {
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render_cmd = "rmarkdown::render('${prefix}.Rmd')"
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}
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"""
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# Dump .params.yml heredoc (section will be empty if parametrization is disabled)
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${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="$task.cpus"
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# Work around https://github.com/rstudio/rmarkdown/issues/1508
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# If the symbolic link is not replaced by a physical file
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# output- and temporary files will be written to the original directory.
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mv "${notebook}" "${notebook}.orig"
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cp -L "${notebook}.orig" "${prefix}.Rmd"
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# Render notebook
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Rscript - <<EOF
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${indent_code_block(render_cmd, 8)}
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writeLines(capture.output(sessionInfo()), "session_info.log")
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EOF
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rmarkdown: \$(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))")
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END_VERSIONS
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"""
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}
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