Bugfix #206
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Bugfix #206
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joshua-slaughter
approved these changes
Oct 2, 2024
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This branch was created to fix a bug in the pipeline, that only occurred on resubmissions of the same job, if there was a global variable that was reassigned to a new value in the first task attempt. For example, in https://github.com/TARGENE/targene-pipeline/blob/main/modules/confounders.nf#L19-L20 :
When this process runs the first time, it executes this line and reassigns the value of qc_file from the value in the input channel (which is a file) to the outcome of this logic (with is a string). Therefore when it retries the process, the value of the variable qc_file is no longer a file, but a string. The task fails to resubmit because .getName() cannot execute on a string.
This happened in filterBED as well as some processes in the extract_traits.nf modules. Please see the referenced issue for clarification.