First encountered by @sidneymbell (so impacting actual users)
If you update Nextclade to v1.10.0 and run nextclade without the --input-dataset flag (which worked in the past) and don't explicitly add --input-virus-properties you get a relatively unspecific error:
[ERROR] Nextclade: Error: File not found: "". Please verify correctness of input flags. If a dataset is used, check that the dataset is not corrupted and is compatible with this version of Nextclade CLI.
When preparing for v1.10.0 we thought about people forgetting to update their datasets, but we didn't think about people who do not use --input-dataset and thus will have to manually add --input-virus-properties.
Since this issue will likely confuse quite a few users, I suggest we make the error more informative, mentioning the file missing explicitly and/or suggesting to use --input-dataset.
In addition, we could make the somewhat breaking change clearer in the changelog to make it easier for people to find out they have to add --input-virus-properties.
I quickly searched Github to check whether people do not use --input-dataset and there's quite a good number of repos. @fritzo has struggled with this, @dpark01 figured it out in the end, and there are more examples, so I think this is quite high priority.
First encountered by @sidneymbell (so impacting actual users)
If you update Nextclade to v1.10.0 and run nextclade without the
--input-dataset
flag (which worked in the past) and don't explicitly add--input-virus-properties
you get a relatively unspecific error:Repro:
When preparing for v1.10.0 we thought about people forgetting to update their datasets, but we didn't think about people who do not use
--input-dataset
and thus will have to manually add--input-virus-properties
.Since this issue will likely confuse quite a few users, I suggest we make the error more informative, mentioning the file missing explicitly and/or suggesting to use
--input-dataset
.In addition, we could make the somewhat breaking change clearer in the changelog to make it easier for people to find out they have to add
--input-virus-properties
.I quickly searched Github to check whether people do not use
--input-dataset
and there's quite a good number of repos. @fritzo has struggled with this, @dpark01 figured it out in the end, and there are more examples, so I think this is quite high priority.Example code: https://github.com/epi2me-labs/wf-artic/blob/master/main.nf#L354 https://github.com/broadinstitute/viral-pipelines/commit/97fd3397479366d7867a8fed6ee1a8cb3e0fa157#diff-3afbf685570ea9a80c1e5eae2b71b260d1c9d27bea5d31138224736974887704 https://github.com/broadinstitute/pyro-cov/commit/5a0abe803539343f8cfa0e17742f12c2177dbbf4 https://github.com/theiagen/public_health_viral_genomics/blob/main/tasks/task_taxonID.wdl