Moritz E. Beber

I had a look and I don't see the same thing when running prefetch from the container. What version of sra-tools are you running? Output that I see: ```sh prefetch...

I think Slack will be easier if you don't mind there's a fetchngs channel.

Since this seems specific to your case, i.e., the content of your NCBI configuration, I suggest you make use of the `args` with a local configuration. ```nextflow process { withName:...

The default behavior is that prefetch creates a directory which contains the SRA so `$id/$id.sra` if you will. This directory is then supplied to fasterq-dump which will look for such...

I'm working on some improvements for the pipeline based on your troubles but it will still take a while until they are released.

Is it possible to somehow detect that an ID comes from ArrayExpress? Or do you think the solution will it be try one thing first and then the other?

The above error message > [ERROR] There is no content for id ERR9539214. Maybe you lack the right permissions? is already the result of special casing 204 so that wouldn't...

Yes, I must admit that I liked the syntax when I saw it at https://diagrams.mingrammer.com/ so I'm all for it! I would only change one thing, I think, if you...

Hi @WLun001, Thanks for the report. That seems a fairly easy addition but I'm currently wrapped up in other work. Would you be able to add these parameters?

Actually, I took a look at the Java and the API definition and these two attributes are not part of the `AutomaticLayout`, it seems.