Updates some of the tasks in the QC pipeline so that checking and copying of the final outputs is performed within the command scripts, rather than being deferred to the finish method of the task.
Specifically the following tasks have been updated:
RunCellrangerCount
RunCellrangerMulti
RunQualimapRnaseq
For tasks such as running cellranger count, prior to this update a failure in one command would mean that none of the outputs were copied to the final destination (meaning that all outputs would have to be regenerated if the pipeline was rerun).
With this change, even if one command in a task fails to complete, the outputs for those that completed successfully will be copied and should not have to be regenerated when rerunning.
Updates some of the tasks in the QC pipeline so that checking and copying of the final outputs is performed within the command scripts, rather than being deferred to the
finishmethod of the task.Specifically the following tasks have been updated:
RunCellrangerCountRunCellrangerMultiRunQualimapRnaseqFor tasks such as running
cellranger count, prior to this update a failure in one command would mean that none of the outputs were copied to the final destination (meaning that all outputs would have to be regenerated if the pipeline was rerun).With this change, even if one command in a task fails to complete, the outputs for those that completed successfully will be copied and should not have to be regenerated when rerunning.