Updates the standalone QC runner utility run_qc.py to allow the user to specify a custom QC protocol, or to customise an existing protocol. via the command line.
The new options are:
--protocol-spec: allows a full QC protocol specification to be supplied
--sequence-reads and --index-reads: allows the reads in a pre-defined protocol to be changed
--qc-modules: allows the QC modules in a pre-defined protocol to be changed
These changes would address some of the issues in #666 (implement QC pipeline as 'mini-protocols') and #638 (enable just the Cellranger count part of a pipeline to be run).
Updates the standalone QC runner utility
run_qc.pyto allow the user to specify a custom QC protocol, or to customise an existing protocol. via the command line.The new options are:
--protocol-spec: allows a full QC protocol specification to be supplied--sequence-readsand--index-reads: allows the reads in a pre-defined protocol to be changed--qc-modules: allows the QC modules in a pre-defined protocol to be changedThese changes would address some of the issues in #666 (implement QC pipeline as 'mini-protocols') and #638 (enable just the Cellranger
countpart of a pipeline to be run).