Harshil Patel

Will close this for now as I suspect the pipeline is being used routinely on human genomes. Be good to know what sort of memory requirements we need to bump...

Added fastp support in https://github.com/nf-core/rnaseq/pull/970 which will allow you to use `--trimmer fastp --extra_fastp_args '--trim_poly_x'` to trim the polyA tails by default along with any adapter sequences.

Don't know how to debug this I'm afraid. If you are able to provide an example of how I can or even better a fix via a PR that would...

Hi @ktrns ! I intentionally left the GTF out from being loaded automatically by IGV because it can take quite a long time to load, especially for the larger genomes....

Closing as unable to reproduce. We also added explicit support for 10x data in https://github.com/nf-core/fetchngs/issues/144 which should hopefully fix the issue. Please feel free to re-open or create a separate...

Hi @Aqsakhalid30 ! Did you manage to solve this issue? As I mentioned in the comment above the best way to run with Singularity is to pull the images beforehand...

Are you aware of a Nextflow implementation that is already using Freyja @poojasgupta @erinyoung ? Be good to eyeball this to scope out adding to this pipeline.

@Joon-Klaps has already created a subworkflow and submitted a PR to nf-core/modules https://github.com/nf-core/modules/pull/3003#pullrequestreview-1336575316 🚀 Will move this to the next milestone in anticipation of adding this at the Hackathon in...

@afonsoguerra @Rohit-Satyam can I confirm that this issue is fixed already by using the code on the `dev` branch please?

Awesome! Thanks for the quick response. Please feel free to submit individual issues for the edge cases you mentioned and we will try to fix in future releases.