Pipeline: log file preservation for failing steps and new backward compatibility system#276

Merged

taimontgomery merged 11 commits intomasterfrom

Feb 3, 2023

Commits on Jan 14, 2023

Removing console capture files from workflow step outputs, and from inputs to subdirectory subworkflows. These are now handled by cwltool's --log-dir option, which has the added benefit of preservi…
AlexTate
committed
Correcting thread count input for preprocessing steps
AlexTate
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Updating run_cwltool_subprocess() to use the --log-dir option so that stdout/stderr captures are preserved for steps that produce errors
AlexTate
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Updating Run Configs with options for naming the new output subdirectory: logs
AlexTate
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Unrelated to issue. This updates the supertest for ensemble GFF validation so that it conforms to the most recent Features Sheet format
AlexTate
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Updating run_cwltool_native() to use the new log_dir RuntimeContext attribute
AlexTate
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