Harshil Patel

Did we find a fix for this @pinin4fjords ? Saw you removed it from the milestone. Shall we push it to the next one?

Will close this for now as we are awaiting further information. Please feel free to re-open if and when you can provide more details. Please feel to join the [#rnaseq](https://nfcore.slack.com/channels/rnaseq)...

I will close this for now, as this looks like more of a generic infrastructure issue. Please feel free to join the [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel in the nf-core Slack Workspace or...

Hi @sebschulz1! Thank you for the beautifully thought-out summary 🤩 I completely agree with you that the pipeline hasn't handled prokaryotic genomes optimally - partly because of poor annotation consistency...

Linking PR here for posterity: https://github.com/nf-core/rnaseq/pull/1191 It still needs some comments addressed, so I will leave this issue open for now.

I am closing this and the linked PR, as it still needs some work to get over the line. Please feel free to re-open both when you have time to...

Hi @charlesfoster @rob-p ! Did you manage to find a solution to this? Is there something we can fix in the pipeline? > $ find . -name "gentrome.fa" -exec ls...

Anyone found a potential cause for this issue? Weird that the index works fine for some samples and not others. Unfortunately, I will need some way of reproducing on my...

Thanks! Latest version of the pipeline (v3.11.2) uses a compatible version: https://github.com/nf-core/rnaseq/blob/5671b65af97fe78a2f9b4d05d850304918b1b86e/modules/nf-core/salmon/quant/main.nf#L5 Be awesome if you can test @charlesfoster @jambler24 and let me know if you still have the same...

Hi @mjsteinbaugh ! Hope you and loved ones are well :) Yes, you are quite right in that the default GRCh38 genome we have available for use is from the...