comparison star_galaxy_outputs.sh @ 1:44632fc0fc15 draft

update

0:a1448d1f2ee4

# change directory to tool outputs directory
cd ${REPORT_FILES_PATH}

# copy outputs from tool outputs directory to corresponding galaxy output path
if [ -e "rmarkdown_report.html" ]; then
  cp rmarkdown_report.html ${REPORT}
fi

if [ -e "index.html" ]; then
  cp index.html ${REPORT}
fi

if [ -e "Aligned.out.sorted.bam" ]; then
  cp index.html ${REPORT}
fi

1:44632fc0fc15

# change directory to tool outputs directory
cd ${REPORT_FILES_PATH}

# copy outputs from tool outputs directory to corresponding galaxy output path
if [ -e "star.html" ]; then
  cp star.html ${REPORT}
fi

if [ -e "index.html" ]; then
  cp index.html ${REPORT}
fi

if [ -e "Aligned.out.sorted.bam" ]; then
  cp Aligned.out.sorted.bam ${X_S}
fi