Refactor to capture exit_status for successful runs #272
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The submission script would incorrectly report a workflow error even when it finished successfully. This was due to the inline exit_status assignment logic, which only captured unsuccessful runs, leaving the exit_status variable unassigned for successful runs. This resulted in an "unbound variable" error message in the logs. To address this issue, we moved the exit_status assignment to the next line (not inline) to ensure that the variable is properly assigned even for successful runs (exit code 0) of the snakemake command. This change resolves the issue and ensures accurate reporting of workflow status. Fixes #262
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The submission script would incorrectly report a workflow error even when it finished successfully. This was due to the inline
exit_statusassignment logic, which only captured unsuccessful runs, leaving theexit_statusvariable unassigned for successful runs. This resulted in an "unbound variable" error message in the logs. To address this issue, we moved theexit_statusassignment to the next line (not inline) to ensure that the variable is properly assigned even for successful runs (exit code 0) of the snakemake command. This change resolves the issue and ensures accurate reporting of workflow status.Fixes #262