slurm_cfg.json

{
    "name": "GCP_slurm_config",
    "version": "2.2",
    "verbose": false,
    "configuration": {
        "memory_limits": {
    	    "aggregate_list":2000,
    	    "assoc_aggregate":16000,
    	    "assoc_combine":6000,
    	    "assoc_plots":24000,
    	    "assoc_report":2000,
    	    "assoc_single":8000,
    	    "assoc_window":20000,
    	    "cleanup":8000,
    	    "combine_variants":8000,
    	    "find_unrelated":8000,
    	    "grm":20000,
    	    "grm_combine":4000,
    	    "ibd_king":8000,
    	    "kinship_plots":8000,
    	    "ld_pruning":51000,
            "merge_gds":12000,
            "null_model":62000,
            "unique_variants":16000,
            "check_merged":16000,
    	    "pca_byrel":8000,
            "pca_corr_vars":4000,
    	    "pca_corr":8000,
    	    "pca_corr_plots":32000,
    	    "pca_plots":2000,
    	    "pcrelate":8000,
            "vcf2gds":8000,
            "post_analysis":2000
        },
        "tasks_per_partition" :{
            "aggregate_list": 8,
    	    "assoc_aggregate": 1,
    	    "assoc_combine": 1,
    	    "assoc_plots": 1,
    	    "assoc_report": 1,
    	    "assoc_single": 1,
    	    "assoc_window": 1,
    	    "cleanup": 1,
    	    "combine_variants": 1,
    	    "find_unrelated": 1,
    	    "grm": 1,
    	    "grm_combine": 1,
    	    "ibd_king": 1,
    	    "kinship_plots": 1,
    	    "ld_pruning": 1,
            "null_model": 1,
            "merge_gds": 1,
            "unique_variants": 1,
            "check_merged": 1,
    	    "null_model": 1,
    	    "pca_byrel": 1,
    	    "pca_corr": 1,
    	    "pca_corr_plots": 1,
    	    "pca_plots": 1,
    	    "pcrelate": 1,
            "vcf2gds": 1,
            "post_analysis": 1
        },
        "pipeline_path_docker": "/usr/local/analysis_pipeline",
        "partition_cfg": "slurm_partitions.json",
        "cluster": "tm1",
        "submit_cmd": "sbatch",
        "submit_log_dir": null,
        "execute_prescript": false,
        "resume_script": "resume_analysis.py",
        "enable_resume": true,
        "dependency_value": "afterok",
        "submit_prescript": "runPython.sh",
        "submit_script": "runDocker.py",
        "submit_opts": {
            "--job-name": null,
            "--array": null,
            "--cpus-per-task": null,
            "--dependency": null,
            "--mem": null,
            "--output": null,
            "--partition": null
        },
        "rdocker_opts": {
            "--dockerimage": "uwgac/topmed-roybranch:latest",
            "--runcmd": null,
            "--runargs": null,
            "--volumes": null,
            "--environment": null,
            "--mem_limit": null,
            "--working_dir": null,
            "--log": false,
            "--machine": null,
            "--cost": null,
            "--verbose": false,
            "--stats": true,
            "--pull": false,
            "--username": null
        },
        "run_cmd": {
            "docker_image": "uwgac/topmed-roybranch:latest"
        }
    }
}