Sherlock optimizations #264
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…mpact on fairshare score
…ures test so others do not have to
…orchestrator job on Sherlock
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When running workflows on Sherlock, the Nextflow process that orchestrates the workflow is submitted to SLURM as a long-running, 1 CPU job that stays alive for the duration of the workflow. It is responsible for submitting additional jobs to SLURM for each task in the workflow. Those tasks must wait in the SLURM queue until a node frees up. All the while, the Nextflow job remains mostly idle. This PR fills this idle CPU time by running certain short workflow tasks (build runtime image, analyses, create variants) directly on the same job as the Nextflow orchestrator, simultaneously avoiding the wait that currently comes with submitting those tasks to the SLURM queue (~15 minute average). I found that after including queue wait time, the ParCa takes about the same time to finish whether it is submitted to the queue as a 4 CPU job or run locally on the 1 CPU Nextflow job. Therefore, I made that run locally as well.
Other changes:
chromosome_segmentunique molecule that is required forsuperhelical_densitysims