Harshil Patel
Harshil Patel
My biggest concern with this is how unwieldy that file is going to get when we go to defining an output schema from a very simple pipeline like fetchngs to...
Did this solution work for you @bmlab-sg ? We could try to incorporate ignoring these sorts of ids via the pipeline but we would need some sort of way to...
Cool. Thanks for the update. We can see if these metadata fields are exposed so we can add conditional filtering to the pipeline in these scenarios so it doesn't hard...
I am unable to reproduce this issue anymore. This could be due to the changes made to the ENA API recently as fixed in https://github.com/nf-core/fetchngs/pull/148 I am now getting `[ERROR]...
Thanks @MatthiasZepper !! > Two issues is down, two to go. I read through your write-up but was a little unclear as to what is still missing here?
@Rohit-Satyam presumably this issue is unrelated to https://github.com/nf-core/viralrecon/issues/321#issuecomment-1292610280 ? @saramonzon is this something we can fix in future releases?
Cool. Will move to the next milestone. Thanks @saramonzon !
Could be solved by #1096
I am able to reproduce this locally when running nf-test: ``` nf-test test --verbose --tag sra_default_parameters --profile test,docker ```
As outlined in https://github.com/ncbi/sra-tools/issues/865#issuecomment-1878538830 `fasterq-dump` is unable to resolve paths that contain a `.` for writing the output files.