where to specify amount of memory?
Hey STQ Team! First of all, thank you for this great Package! If I can get it to work this will greatly help my work. I recently ran my first PDX Visium Experiment and was trying to run your Nextflow pipeline on a HPC (slurm submission). I adapted the node specification in the submit.sb script and the nextflow.config files. Unfortunately I ran into some more issues when trying to run the Demo. This is the execution error that I got. The memory specification is specified in the submit.sb
Error executing process > 'TWO:SEQ:LOAD_SAMPLE_INFO (Demo_S1)'
Caused by: Failed to submit process to grid scheduler for execution
Command executed:
sbatch .command.run
Command exit status: 1
Command output: sbatch: error: Mem flag not set for partial node allocation. sbatch: error: Please specify the amount of memory for the job with: "--mem xxG". sbatch: error: Batch job submission failed: Job size specification needs to be provided
Any Help will be greatly appreciated! Thank you! All the best, Patrick