Jonathan Manning

Just for my info, is there any prospect of this being addressed in the near future? The inability to instantly delete intermediates (as e.g. Snakemake can do) is hitting us...

Just to check, does your local machine have sufficient resource? STAR_ALIGN is labelled [process_high](https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/modules/nf-core/star/align/main.nf#L3), [which means](https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/conf/base.config#L42) it needs 72GB RAM.

People tend not to run these workflows on one big local machine, so I don't have much experience to draw on. But I occasionally saw this sort of thing happen...

Do you also have the STAR logs from the process directory? Also, just to be clear, something like `--max_memory '64.GB'` sets the maximum bounds on memory for the workflow as...

I think it's quite likely HISAT2 is failing for some reason with those input data, which is causing the pipe error, see this Slack thread: https://nfcore.slack.com/archives/CE8SSJV3N/p1713885189645209. I would start with...

This is likely to be because you are using `--genome mm10`, which will pull a pre-built index. You should see a warning like this in the workflow run: ``` WARN:...

Note that we currently r[ecommend against](https://nf-co.re/rnaseq/3.14.0/docs/usage#explicit-reference-file-specification-recommended) use of igenomes (i.e. `--genome`), since the reference files in iGenomes are vastly out of date. You will be better served by specifying up...

Also, 3.10 is quite old now. I'd suggest using the latest release if you can.

The process selector was incorrect in the OP. You should have specified: ```NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN``` while you specified ```NFCORE_RNASEQ:RNASEQ:ALIGN_STAR``` (`align_star` is just the subworkflow in this case, so the selector wasn't hitting...

Liking this. If we really need the output block (rather than doing something with emit), this is a nice readable way of doing it.