Harshil Patel

Thanks for reporting @peterk87! Not sure what the best solution is here because by default the pipeline will and has always used the same reference fasta and annotation for reproducibility....

Most other resources like the ARTIC primer sets etc all use `MN908947.3` by default which is why it made sense to pick that. It meant we could just point to...

Nice! Thanks @saramonzon @peterk87 are you able to download the latest annotation for `MN908947.3` and confirm that it fixes the issue for you?

I have downloaded the latest GFF file for `MN908947.3` and I can't see a difference in the primary annotation which probably means it won't fix this issue. I have attached...

Thanks @peterk87 ! That is very helpful. Not sure what to do about this since most of the standard annotations don't have an explicit entry for `ORF1b`. Will leave this...

Hi @Mewgia ! I have seen this error too and I still haven't got to the bottom of it. For some reason SPAdes fails when I run the pipeline on...

This is what I see: ``` $ cat .command.log tput: No value for $TERM and no -T specified tput: No value for $TERM and no -T specified tput: No value...

Unfortunately not @josruirod. Needs some more digging to figure out what is going on. Quietly hoping someone beats me to it!

Thats what I was thinking. So we can put them in `nf-core/configs/docs/configuration/`? Thats where they are currently kept for other pipelines. If someone decides to add a custom config how...

I have added the docs for the Crick in the `nf-core/configs/docs/` folder. See https://github.com/nf-core/configs/pull/7 We need to add docs for the rest of the configs currently hosted in the repository...