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TheRoddyWMS / Roddy

The Roddy workflow development and management system.
http://roddy-documentation.readthedocs.io
MIT License
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`debugOptionsUseUndefinedVariableBreak` broken #184

Open vinjana opened 6 years ago

vinjana commented 6 years ago

The runtimeConfig.sh that is still sourced, although the .parameter files contain all variables, may contain undefined variables. Thus the debugOptionsUseUndefinedVariableBreak option breaks the script in the runtimeConfig.sh.

dankwart-de commented 6 years ago

The runtime config is not sourced anymore. I'll close this now.

vinjana commented 6 years ago

Negative. The problem persists with the job-parameter files. Indeed the problems with sample, run etc. that I recently mentioned and partially fixed were related to this issue (so the feature itself is useful). The problem further is relevant for situations where e.g. general global configuration values (such as sequenceDirectory in the CO configs) reference variables that are only relevant in specific jobs, e.g. library in jobs working with tagmentation lanes, run in per-lane alignment jobs. For other jobs, such as merging jobs, these variables don't make sense and cannot be set to a reasonable value!

dankwart-de commented 6 years ago

Ok, then I am sorry for closing this too fast :D.

vinjana commented 6 years ago

For now the problem is postponed. We will fix this when changing the CORuntimeService class.

The idea is to always have checks turned on. We may consider changing Roddy in certain ways to resolve this problem.