Updates the QC pipeline (in qc/pipeline.py) to explicitly define a job runner for Picard tools (picard), where previously the default runner was used.
Also adds support for the picard runner to be specified in the [runners] section of the configuration file (in settings.py), and for this setting to be passed to the pipeline from the run_qc command (in commands/run_qc_cmd.py) and the standalone run_qc.py utility (cli/run_qc.py).
The sample config file has not been updated, however the configuration documentation now includes the picard runner in the appropriate table.
Updates the QC pipeline (in
qc/pipeline.py) to explicitly define a job runner for Picard tools (picard), where previously the default runner was used.Also adds support for the
picardrunner to be specified in the[runners]section of the configuration file (insettings.py), and for this setting to be passed to the pipeline from therun_qccommand (incommands/run_qc_cmd.py) and the standalonerun_qc.pyutility (cli/run_qc.py).The sample config file has not been updated, however the configuration documentation now includes the
picardrunner in the appropriate table.