Make submission date optional #691
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Metadata typically includes the 'submission_date' field, which was used in two rules: `diagnostic` and `recency`. The latter rule proceeded without error if the metadata field was missing (albeit producing a non-useful output) but the former required the field to exist. This has prevented people from running the pipeline [1]. This commit allows the diagnostic step to proceed without the 'submission_date' field, printing a warning message instead. [1] https://discussion.nextstrain.org/t/error-in-main-workflow-smk-file-in-latency-wait/616
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huddlej
approved these changes
Aug 4, 2021
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Metadata typically includes the 'submission_date' field, which was used
in two rules:
diagnosticandrecency. The latter rule proceededwithout error if the metadata field was missing (albeit producing
a non-useful output) but the former required the field to exist. This
has prevented people from running the pipeline.
This commit allows the diagnostic step to proceed without the
'submission_date' field, printing a warning message instead.