aws_batch_cfg.json

{
    "name": "AWS_Batch_config",
    "version": "3.3",
    "debug": 0,
    "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,
            "unique_variants":16000,
            "check_merged":16000,
    	    "null_model":51000,
    	    "pca_byrel":8000,
    	    "pca_corr":8000,
    	    "pca_corr_plots":32000,
    	    "pca_plots":2000,
    	    "pcrelate":8000,
            "vcf2gds":8000
        },
        "autogen_ce": "No",
        "aws_profile": "nhlbi_compute",
        "pricing": "EC2",
        "batch_instances": "",
        "pipeline_path": "/usr/local/analysis_pipeline",
        "queue": "topmed_general_od",
        "maxperf": 0,
        "resume_script": "resume_analysis.py",
        "enable_resume": false,
        "job_parameters": {
            "wd" : "",
            "rd" : "tbd",
            "ra" : "tbd",
            "lf" : "runrscript.log",
            "bm" : "1",
            "tmo": "60",
            "db" : "1",
            "po" : "0",
            "at" : "0",
            "mc" : "not used",
            "tf" : "1"
        },
        "submit_opts": {
            "jobdef": "TM_roybranch",
            "vcpus":  1,
            "memory": 5000,
            "dependsOn": [],
            "command": []
        },
        "retryStrategy": {
            "attempts": 1
        },
        "sync_job": {
            "parameters": {
                "msg": "Dependent jobs completed\n",
                "jids": ""
            },
            "submit_opts": {
                "jobdef": "TM_sync",
                "dependsOn": []
            }
        },
        "run_cmd": {
            "docker_image": "uwgac/topmed-roybranch:latest"
        }
    }
}