Updates to src/nextflow.config
I'm newish to nextflow, but have implemented a few differences in my own config file used on PSMN compared to the one here, and wanted to discuss with you:
- I restored
charliecloud
prefixes forreadOnlyInputs
andcacheDir
- why are they not prefixed bycharliecloud
? - Remove
--bind
ing as nextflow takes care of it, stated here:Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files.
- Use
queue
notclusterOptions
for Lake partition, as per here:SLURM partitions can be considered jobs queues. Nextflow allows you to set partitions by using the above queue directive.
- Use
slurm
executor always underprocess
- why do you only addslurm
for the labelled processes, not for all processes underpsmn
profile?
I wouldn't insist that any of these suggestions be integrated, or know for sure they are correct