Currently, pipelines including trimming (and when --no-trim is not provided) will first trim on upload, and then attempt to trim on the cluster. This is happening because bin/distmap is calling Utility::get_steps, which in turn constructs a HadoopTrimming object here:
magicDGS
commented
6 years ago
Currently, pipelines including trimming (and when
--no-trimis not provided) will first trim on upload, and then attempt to trim on the cluster. This is happening becausebin/distmapis callingUtility::get_steps, which in turn constructs aHadoopTrimmingobject here:https://github.com/robmaz/distmap/blob/dd1b577526d4190fa22178fa67b8690483908a97/lib/perl5/site_perl/Utility.pm#L444-L450
Also, if the whole pipeline is requested,
bin/distmapcallsUtility::run_whole_pipelineand adds trimming to it:https://github.com/robmaz/distmap/blob/dd1b577526d4190fa22178fa67b8690483908a97/lib/perl5/site_perl/Utility.pm#L397-L401
This should be removed to make trimming works as expected in the beta version.