# HG changeset patch
# User mingchen0919
# Date 1526308899 14400
# Node ID 851112a0071d379ad758a2f4cfd9648347489764
# Parent  650f71d8fc4e91f2a23f6caffc3dcc9de13c15dd
planemo upload commit 8758ce271d51387da37298280356fb3f34c4db49-dirty

diff -r 650f71d8fc4e -r 851112a0071d expose-outputs-to-galaxy-history.sh
--- a/expose-outputs-to-galaxy-history.sh	Tue May 01 11:27:37 2018 -0400
+++ b/expose-outputs-to-galaxy-history.sh	Mon May 14 10:41:39 2018 -0400
@@ -10,4 +10,6 @@
   cp index.html ${REPORT}
 fi
 
-cp count_data.csv ${X_c}
\ No newline at end of file
+if [ -e "count_data.csv" ];then
+  cp count_data.csv ${X_c}
+fi
\ No newline at end of file
diff -r 650f71d8fc4e -r 851112a0071d rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Tue May 01 11:27:37 2018 -0400
+++ b/rmarkdown_report.Rmd	Mon May 14 10:41:39 2018 -0400
@@ -56,7 +56,7 @@
 ## Job script
 
 ```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
+sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
 ```
 
 ```{r echo=FALSE, comment='', results='asis'}