clean up fastqc mess
remove logging level setting
mv Tuxedo-specific templates out of shared folder
remove duplicated files, use ngcloud builtin
use ngcloud.pipe to construct GATK pipeline
add a hack to include local folder Python package
put report to standard pipeline template structure
add custom copytree that allow existed directories
remove noused custom abspath
remove use of custom abspath with Path.resolve()
use custom merge_copytree to copy static files