Harshil Patel
Harshil Patel
If you supply the pipeline with just a `--fasta` and `--gtf` and providing that the non-coding transcripts are defined in the GTF file (I believe they are in ENSEMBL GTF)...
Hi @mjsteinbaugh ! Just tidying up issues before tomorrow's release. Is this ok to close?
Seeing the same issue too on WSL2 using the version @swingingsimian reported.
Yo! Why doesn't the current behaviour of copying a directory work here? This would have been tested already on Azure?
Merging this in will need some thought because this will change the way we are dealing with indices in pipelines quite a bit and how they are defined by users....
But it should just be a directory no? This should then affect any directory defined as output on Azure?
Done! https://github.com/nf-core/configs/commit/f84bc302a1b22e6b4654714f280b31ef7b0bf3b6 Are you able to test it out with the latest version of the pipeline and let us know if everything is working as expected please?
Yep, this is a more complex issue with the way parameters are coerced by Nextflow and then mismatch the validation. Changing the line below to `string` does fix error above:...
In general though, if you plan on using this primer set even more often it's worth downloading the files locally and updating the `-params-file` so you don't download the files...
Ok. Ignore everything I said about using a params file. Can you try with your original command in [this comment](https://github.com/nf-core/viralrecon/issues/373#issuecomment-1482682063) and add this parameter too please? `--schema_ignore_params 'genomes,primer_set_version' ` Thanks...