mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
88 lines
3.4 KiB
Text
88 lines
3.4 KiB
Text
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
|
|
"""
|
|
}
|