Hi all! I'd like to change slightly the way we handle

--genome

/ igenomes. This is motivated by an error @Felix Krueger flagged, caused by my assuming that anyone using

--genome

was using iGenomes, whereas he very reasonably uses his own genome config compatible with up-to-date STAR. I actually replaced an old check based on file names that was brittle and causing problems. So https://github.com/nf-core/rnaseq/pull/1834 re-pitches the functionality to allow for more flexibility. The currently distributed

genomes.config

entries now have a 'legacy' flag on all the genomes so that the pipeline knows to use the older STAR with those indices. Folks can still use their own genome setup without that flag and it'll all be fine. Would really appreciate review if anyone has time, and folks here are more qualified than most! Then we're almost ready to release with the new shiny TrimGalore goodness 🙂

I have resumed yesterday’s failed run with the new branch, and it now launches a new task

NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN_LEGACY

, however it fails still with:

May 06 13:08:59 ..... started STAR run
May 06 13:09:01 ..... loading genome
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "genomeType" in input "genomeParameters.txt"
SOLUTION: use correct parameter name (check the manual)
May 06 13:09:01 ...... FATAL ERROR, exiting

Lemme just see if I can spot why this isn't fixing it ....

ok

By way of explanation, what Felix was doing was overlaying, rather than replacing the igenomes config, which was a risky proposition in any case. Thanks for the assistance Felix!

shared a GIF

I was concerned at first when I read the first message, but then I saw the code

This was even more improved by the later PR which removed the legacy STAR entirely