Hi! does anyone know if/when nf-sarek will work with nextflow version 26.04.1? currently there is a parsing error. I am also getting a problem with the sarek pipeline where my machine only has 14 cores and my --max_cpus 14 flag is detected as an invalid input but the sarek docs do have this an option. Thanks!

Hey! Until we release you'll need to set `

export NXF_SYNTAX_PARSER=v1

--max_cpus

has been deprecated for a while, use

resourceLimits

instead: https://docs.seqera.io/nextflow/reference/process#resourcelimits

Thank you so much!

Beware that resourceLimits will limit only per process (if I understood well), for the whole run you need to also set

executor {
    name = 'local'
    cpus = 14
    memory = '80 GB'  // optional: total memory limit
}

The last should only be needed if you want to use lower total consumption limits than provided by your machine. And by themselves they don't do much as nextflow doesn't enforce any limits by itself, only uses them to figure out if it can start more jobs, but if you use e.g.

docker

as a container engine, nextflow will pass them along and docker will enforce them.