Mercurial > repos > mingchen0919 > elastic_expose_data

diff individuals_render.R @ 4:9ff33a3631fa draft

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planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
author mingchen0919
date Mon, 02 Apr 2018 08:32:59 -0400
parents 5838300fc1aa
children
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--- a/individuals_render.R	Mon Apr 02 00:32:04 2018 -0400
+++ b/individuals_render.R	Mon Apr 02 08:32:59 2018 -0400
@@ -19,9 +19,12 @@
 # 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'), '/paired.Rmd'),
+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