nf-core_modules/modules/rmarkdownnotebook/main.nf

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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-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
'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 - <<EOF
${indent_code_block(render_cmd, 8)}
writeLines(capture.output(sessionInfo()), "session_info.log")
EOF
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rmarkdown: \$(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))")
END_VERSIONS
"""
}