comparison individuals_render.R @ 4:9ff33a3631fa draft

planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty

3:5838300fc1aa

#------------------------------------------------
# create three folders within working directory
dir.create('individual_outputs')

#-----------------render Rmd--------------
# copy R markdown file to working directory and render it within the working directory.
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/paired.Rmd'),
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the

4:9ff33a3631fa

#------------------------------------------------
# create three folders within working directory
dir.create('individual_outputs')

job_working_dir = getwd()
individual_outputs_path = paste0(job_working_dir, '/individual_outputs/')

#-----------------render Rmd--------------
# copy R markdown file to working directory and render it within the working directory.
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/individuals.Rmd'),
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the