include { dump_params_yml; indent_code_block } from "./parametrize" process RMARKDOWNNOTEBOOK { tag "$meta.id" label 'process_low' //NB: You likely want to override this with a container containing all required //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : 'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }" 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 tuple val(meta), path ("session_info.log"), emit: session_info path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params // Dump parameters to yaml file. // Using a yaml file over using the CLI params because // * no issue with escaping // * allows to pass nested maps instead of just single values def params_cmd = "" def render_cmd = "" if (parametrize) { nb_params = [:] if (implicit_params) { nb_params["cpus"] = task.cpus nb_params["artifact_dir"] = "artifacts" nb_params["input_dir"] = "./" } if (meta_params) { nb_params["meta"] = meta } nb_params += parameters params_cmd = dump_params_yml(nb_params) render_cmd = """\ params = yaml::read_yaml('.params.yml') rmarkdown::render('${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 - < versions.yml "${task.process}": rmarkdown: \$(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))") END_VERSIONS """ }