Jobs and ThreadsΒΆ

Most steps of the workflow are utilizing applications that can thread or otherwise use multiple cores. Leaving this one below the max, in cases where many samples are being analyzed, may be optimal as single-threaded jobs will be processed more efficiently.


Threads is used per step and will most likely be a subset of --jobs. --jobs represents the total available cores for all simultaneous steps.

Default: 1

threads: 23

When starting your atlas command, e.g. atlas assemble --jobs 48 config.yaml, be sure to set the total thread pool to capture all available possible jobs to be executed simultaneously. For example, if we are utilizing 3 nodes, each with 24 cores, we would set threads: 24 and execute atlas with:

atlas assemble --jobs 72 config.yaml