Question about Nextflow and SLURM

I’m new to Nextflow and HPC computing so I have a question about Nextflow and SLURM. Can SLURM syntax be slightly different between HPCs? If so, then if running Nextflow or an nf-core pipeline using SLURM, how does Nextflow know exactly how to write the SLURM job script for a given process on the system you’re using? Is this something that needs to be configured using an institutional profile?

The syntax for SLURM should not be different between HPCs. Different workloadm managers will have different syntaxes thouhg (PBS Torque, SLURM, etc) but if you tell Nextflow which one you’re using, it will build the correct script to launch the jobs :wink:

Institutional profiles are useful not for the SLURM syntax but particularities such as available resources, queue/partition names and so on. You can check some examples here (See the bottom of the README file for a list of institutions and the corresponding instructions to run Nextflow there).