Running PHoeNIx on Different Systems

How do I Adjust CPUs/Memory Usage?

Nextflow uses config files to determine how many CPUs/Memory to give to jobs which are all found in the conf folder. The test profile has it own config that can be edited to speed up the test sample as its just limited to 2 CPUs.

PHoeNIx is structured so that each process that is run is "labeled" high, medium or low. See SPAdes as and example. The CPUs/Memory requirements are then determined by the process labels in the base.config file. Editing the CPUs/Memory in the base.config for a label well cause all process with that label to use those resources.

If you used git clone for your install then simply edit the base.config file and save it in the same place and you are good to go. However, if you used nextflow run or are running on nextflow tower the best way to change the number of CPUs/Memory for each process is to create a new config file with labels like the base.config and pass it to nextflow with the -c command on CLI.

Configuration for Running PHoeNIx on a High Performance Computing (HPC) Cluster

To run PHoeNIx on an HPC and submit jobs to a cluster you will need to make config file for your executor. We provide a template in the conf folder to edit. How to pass this to PHoeNIx depends on the type of install you are using. For full details on configs see nextflow documentation.

If you used git clone to install

After editing the template in the conf folder you save it in the same place and then run PHoeNIx with:

nextflow run $PATH_TO_INSTALL/phoenix -entry PHOENIX -profile singularity,custom_HPC --input samplesheet.csv --kraken2db $PATH_TO_DB

If you used nextflow pull or nextflow run to install

After editing the template in the conf folder, then you save it to a new location passing it the PHoeNIx with the -c parameter. Now you can run PHoeNIx with:

nextflow run cdcgov/phoenix -r v1.0.0 -entry PHOENIX -profile singularity -c mycustom_config.config --input samplesheet.csv --kraken2db $PATH_TO_DB