I received a bug report for minimap2/align bundled samtools command github.com/nf-core/genomeassembler/issues/265 and I am a bit surprised that this hasnt surfaced before, could someone who is into samtools take a quick look?

Given the issue they reference is 5 years old and has a supposed fix via a PR I am sceptical if it is actually that bug, although the error message does seem to indicate it could be.

Thanks!

You can ask if they can provide the

.command.sh

that the task ran so someone can see if they can recreate the issue with some dummy data