When users run a pipeline with the .run method the parameter pars file setting are not used. It is recommended to use the .call method because this method uses the setting set in the various parameter referenced files. Users still have been using the .run method (usually by mistake) which can lead to steps that are usually skipped in a parameter reference file are used in the .run method. By setting skip = True for default in the spec of the step the default would be to skip the step - even if the .run method is used. This was useful for the mrs_imatch step. It could be useful for IPC and reset step as well as other steps. By manually setting skip=False the user can still invoke the step.
This ticket is to review which steps could have the default skip = True set in the step and add that to the spec of those steps.
Issue JP-3720 was created on JIRA by Jane Morrison:
When users run a pipeline with the .run method the parameter pars file setting are not used. It is recommended to use the .call method because this method uses the setting set in the various parameter referenced files. Users still have been using the .run method (usually by mistake) which can lead to steps that are usually skipped in a parameter reference file are used in the .run method. By setting skip = True for default in the spec of the step the default would be to skip the step - even if the .run method is used. This was useful for the mrs_imatch step. It could be useful for IPC and reset step as well as other steps. By manually setting skip=False the user can still invoke the step.
This ticket is to review which steps could have the default skip = True set in the step and add that to the spec of those steps.