Jennifer Chang

Do we want to also support and document the following formats? * `YYYY-MM (Day unknown)` * `YYYY (Month and day unknown)` Fauna's [format_date](https://github.com/nextstrain/fauna/blob/2428cfd7a72487d99fe149bb0689536bab165e76/vdb/upload.py#L190) function seems to process it, but I...

Of the five cases, I've maybe seen 1 and 5: * case 1: `2020-01-X1` - someone has a bug in their curation script before they passed me the file. I'm...

[non-blocking comment] I see we're changing "runner.sh", not sure if we want to make it `--cores all` for all the snakemake calls: * https://github.com/search?q=org%3Anextstrain+%22snakemake%22+%22--cores+1%22&type=code

Makes sense. Help statement indicates a 0 value should be valid [augur/mask.py#L172](https://github.com/nextstrain/augur/blob/master/augur/mask.py#L172) and as far as I can tell shouldn't break the `mask_sequence` function in [augur/mask.py#L78](https://github.com/nextstrain/augur/blob/15dfc8bc5c5a570066ddd5601c9aa82e0c1d2b7d/augur/mask.py#L78) Seems to be thrown...

> I don't expect the data with underscores to be an issue because the GISAID data downloaded with that option will have underscores in both metadata and sequences Just a...

I lean toward possible solution 2, but I'm probably missing the historical context.

Thanks for the message! Could you run the following to see if it returns the same error? ``` nextflow -version ``` I have a suspicion that it's related to this...

Ah I see what's happening, the polishCLR_env on your system would need to be activated using: ``` conda activate /home/cbfgws6/Programs/nextflow/env/polishCLR_env ``` But could you run a `which java` before and...

Since this seems to be an ongoing issue with Nextflow & conda and I am not a maintainer of Nextflow. * https://github.com/nextflow-io/nextflow/issues/1523 I highly recommend trying the docker or singularity...

Could add guard-rails here to throw an error if the user passes in a fasta file instead of the required bam file: https://github.com/isugifNF/polishCLR/blob/d1a1b9f8b08132a6f5715f774c0ddb915983bdce/main.nf#L227-L236