Unable to initialize nextflow environment on Sanger HPC

[matbeale]

Hi team,

I decided to have a play with nano-rave for some of my amplicon work. However, I'm encountering immediate issues getting the nextflow to actually run (I've not encountered this one before on farm). Any ideas?

Thanks,
Mat

[flass]

Hi Mat,

can you please run again the code with the suggested debug flag -Dcapsule.log=verbose ?

what version of nano-rave are you running? or if appropriate, what farm module have you loaded for it?
also what is you environment like when you run it? can you please give us the output of module list and any other environment modifier (conda env, bash env variables) you may have set?

it might be something wrong with the Nextflow version