From de721d4edf3b3248c94a19fd103d6c63a9ea5962 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Fri, 15 Nov 2024 10:09:08 -0800
Subject: [PATCH 01/11] Add resources.json

---
 config/resources.json | 1274 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 1274 insertions(+)
 create mode 100644 config/resources.json

diff --git a/config/resources.json b/config/resources.json
new file mode 100644
index 0000000..f4959d1
--- /dev/null
+++ b/config/resources.json
@@ -0,0 +1,1274 @@
+{
+    "f2": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.5,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.26,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.5,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.26,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.5,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.26,
+                "max": "1 GB"
+            }
+        }
+    },
+    "f16": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        },
+        "run_RealignerTargetCreator_GATK": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.13,
+                "max": 2
+            },
+            "memory": {
+                "min": "4 GB",
+                "fraction": 0.13,
+                "max": "4 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_IndelRealigner_GATK": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.13,
+                "max": 2
+            },
+            "memory": {
+                "min": "4 GB",
+                "fraction": 0.13,
+                "max": "4 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_BaseRecalibrator_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "30 GB",
+                "fraction": 0.99,
+                "max": "30 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_ApplyBQSR_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.07,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_MergeSamFiles_Picard": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.13,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.26,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "deduplicate_records_SAMtools": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.13,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.26,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_index_SAMtools": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.07,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_GetPileupSummaries_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.16,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_CalculateContamination_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.16,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_DepthOfCoverage_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.16,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "remove_intermediate_files": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        },
+        "remove_unmerged_BAMs": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        },
+        "remove_merged_BAM": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.06,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.03,
+                "max": "1 GB"
+            }
+        }
+    },
+    "f32": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        },
+        "run_RealignerTargetCreator_GATK": {
+            "cpus": {
+                "min": 4,
+                "fraction": 0.13,
+                "max": 4
+            },
+            "memory": {
+                "min": "6 GB",
+                "fraction": 0.10,
+                "max": "6 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_IndelRealigner_GATK": {
+            "cpus": {
+                "min": 4,
+                "fraction": 0.13,
+                "max": 4
+            },
+            "memory": {
+                "min": "6 GB",
+                "fraction": 0.10,
+                "max": "6 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_BaseRecalibrator_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "60 GB",
+                "fraction": 0.99,
+                "max": "60 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_ApplyBQSR_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.03,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_MergeSamFiles_Picard": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.06,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.13,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "deduplicate_records_SAMtools": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.06,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.13,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_index_SAMtools": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.03,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_GetPileupSummaries_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.08,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_CalculateContamination_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.08,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_DepthOfCoverage_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
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+                "fraction": 0.16,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "remove_intermediate_files": {
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+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        },
+        "remove_unmerged_BAMs": {
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+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        },
+        "remove_merged_BAM": {
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+                "fraction": 0.03,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.02,
+                "max": "1 GB"
+            }
+        }
+    },
+    "f72": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
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+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
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+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "run_RealignerTargetCreator_GATK": {
+            "cpus": {
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+                "fraction": 0.08,
+                "max": 6
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_IndelRealigner_GATK": {
+            "cpus": {
+                "min": 6,
+                "fraction": 0.08,
+                "max": 6
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_BaseRecalibrator_GATK": {
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+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
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+                "fraction": 0.53,
+                "max": "72 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_ApplyBQSR_GATK": {
+            "cpus": {
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+                "fraction": 0.01,
+                "max": 1
+            },
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+                "fraction": 0.01,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_MergeSamFiles_Picard": {
+            "cpus": {
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+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.06,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "deduplicate_records_SAMtools": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.06,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_index_SAMtools": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.01,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_GetPileupSummaries_GATK": {
+            "cpus": {
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+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.04,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_CalculateContamination_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.04,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_DepthOfCoverage_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "remove_intermediate_files": {
+            "cpus": {
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+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "remove_unmerged_BAMs": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "remove_merged_BAM": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        }
+    },
+    "m64": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.00,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.00,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.00,
+                "max": "1 GB"
+            }
+        },
+        "run_RealignerTargetCreator_GATK": {
+            "cpus": {
+                "min": 4,
+                "fraction": 0.06,
+                "max": 4
+            },
+            "memory": {
+                "min": "30 GB",
+                "fraction": 0.03,
+                "max": "30 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_IndelRealigner_GATK": {
+            "cpus": {
+                "min": 4,
+                "fraction": 0.06,
+                "max": 4
+            },
+            "memory": {
+                "min": "30 GB",
+                "fraction": 0.03,
+                "max": "30 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_BaseRecalibrator_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "500 GB",
+                "fraction": 0.51,
+                "max": "500 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_ApplyBQSR_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.00,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_MergeSamFiles_Picard": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.01,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "deduplicate_records_SAMtools": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.01,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_index_SAMtools": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.00,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_GetPileupSummaries_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.01,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_CalculateContamination_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.01,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_DepthOfCoverage_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.02,
+                "max": 1
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.01,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        }
+    },
+    "default": {
+        "run_validate_PipeVal": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "extract_GenomeIntervals": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "run_SplitIntervals_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "run_RealignerTargetCreator_GATK": {
+            "cpus": {
+                "min": 6,
+                "fraction": 0.08,
+                "max": 6
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_IndelRealigner_GATK": {
+            "cpus": {
+                "min": 6,
+                "fraction": 0.08,
+                "max": 6
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_BaseRecalibrator_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "72 GB",
+                "fraction": 0.53,
+                "max": "72 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_ApplyBQSR_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.01,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 4
+                }
+            }
+        },
+        "run_MergeSamFiles_Picard": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.06,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "deduplicate_records_SAMtools": {
+            "cpus": {
+                "min": 2,
+                "fraction": 0.03,
+                "max": 2
+            },
+            "memory": {
+                "min": "8 GB",
+                "fraction": 0.06,
+                "max": "8 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_index_SAMtools": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "2 GB",
+                "fraction": 0.01,
+                "max": "2 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_GetPileupSummaries_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.04,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_CalculateContamination_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "5 GB",
+                "fraction": 0.04,
+                "max": "5 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "run_DepthOfCoverage_GATK": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "10 GB",
+                "fraction": 0.07,
+                "max": "10 GB"
+            },
+            "retry_strategy": {
+                "memory": {
+                    "strategy": "exponential",
+                    "operand": 2
+                }
+            }
+        },
+        "remove_intermediate_files": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "remove_unmerged_BAMs": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        },
+        "remove_merged_BAM": {
+            "cpus": {
+                "min": 1,
+                "fraction": 0.01,
+                "max": 1
+            },
+            "memory": {
+                "min": "1 GB",
+                "fraction": 0.01,
+                "max": "1 GB"
+            }
+        }
+    }
+}
\ No newline at end of file

From 096d7e6df77fd4cdda058e7c158d5fb68fdd8675 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Fri, 15 Nov 2024 10:12:55 -0800
Subject: [PATCH 02/11] Delete node-specific configs

---
 config/F16.config | 126 ----------------------------------------------
 config/F2.config  |  14 ------
 config/F32.config | 126 ----------------------------------------------
 config/F72.config | 126 ----------------------------------------------
 config/M64.config | 114 -----------------------------------------
 5 files changed, 506 deletions(-)
 delete mode 100644 config/F16.config
 delete mode 100644 config/F2.config
 delete mode 100644 config/F32.config
 delete mode 100644 config/F72.config
 delete mode 100644 config/M64.config

diff --git a/config/F16.config b/config/F16.config
deleted file mode 100644
index 82762e9..0000000
--- a/config/F16.config
+++ /dev/null
@@ -1,126 +0,0 @@
-process {
-    withName: run_validate_PipeVal {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: extract_GenomeIntervals {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_SplitIntervals_GATK {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_RealignerTargetCreator_GATK {
-        cpus = 2
-        memory = 4.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_IndelRealigner_GATK {
-        cpus = 2
-        memory = 4.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_BaseRecalibrator_GATK {
-        cpus = 1
-        memory = 30.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_ApplyBQSR_GATK {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_MergeSamFiles_Picard {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: deduplicate_records_SAMtools {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_index_SAMtools {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_GetPileupSummaries_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_CalculateContamination_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_DepthOfCoverage_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: remove_intermediate_files {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_unmerged_BAMs {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_merged_BAM {
-        cpus = 1
-        memory = 1.GB
-    }
-}
diff --git a/config/F2.config b/config/F2.config
deleted file mode 100644
index b20f6dd..0000000
--- a/config/F2.config
+++ /dev/null
@@ -1,14 +0,0 @@
-process {
-    withName: run_validate_PipeVal {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: extract_GenomeIntervals {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_SplitIntervals_GATK {
-        cpus = 1
-        memory = 1.GB
-    }
-}
diff --git a/config/F32.config b/config/F32.config
deleted file mode 100644
index d96e1b7..0000000
--- a/config/F32.config
+++ /dev/null
@@ -1,126 +0,0 @@
-process {
-    withName: run_validate_PipeVal {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: extract_GenomeIntervals {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_SplitIntervals_GATK {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_RealignerTargetCreator_GATK {
-        cpus = 4
-        memory = 6.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_IndelRealigner_GATK {
-        cpus = 4
-        memory = 6.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_BaseRecalibrator_GATK {
-        cpus = 1
-        memory = 60.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_ApplyBQSR_GATK {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_MergeSamFiles_Picard {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: deduplicate_records_SAMtools {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_index_SAMtools {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_GetPileupSummaries_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_CalculateContamination_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_DepthOfCoverage_GATK {
-        cpus = 1
-        memory = 10.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: remove_intermediate_files {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_unmerged_BAMs {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_merged_BAM {
-        cpus = 1
-        memory = 1.GB
-    }
-}
diff --git a/config/F72.config b/config/F72.config
deleted file mode 100644
index 8007e15..0000000
--- a/config/F72.config
+++ /dev/null
@@ -1,126 +0,0 @@
-process {
-    withName: run_validate_PipeVal {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: extract_GenomeIntervals {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_SplitIntervals_GATK {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_RealignerTargetCreator_GATK {
-        cpus = 6
-        memory = 10.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_IndelRealigner_GATK {
-        cpus = 6
-        memory = 10.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_BaseRecalibrator_GATK {
-        cpus = 1
-        memory = 72.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_ApplyBQSR_GATK {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_MergeSamFiles_Picard {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: deduplicate_records_SAMtools {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_index_SAMtools {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_GetPileupSummaries_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_CalculateContamination_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_DepthOfCoverage_GATK {
-        cpus = 1
-        memory = 10.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: remove_intermediate_files {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_unmerged_BAMs {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: remove_merged_BAM {
-        cpus = 1
-        memory = 1.GB
-    }
-}
diff --git a/config/M64.config b/config/M64.config
deleted file mode 100644
index f47e323..0000000
--- a/config/M64.config
+++ /dev/null
@@ -1,114 +0,0 @@
-process {
-    withName: run_validate_PipeVal {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: extract_GenomeIntervals {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_SplitIntervals_GATK {
-        cpus = 1
-        memory = 1.GB
-    }
-    withName: run_RealignerTargetCreator_GATK {
-        cpus = 4
-        memory = 30.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_IndelRealigner_GATK {
-        cpus = 4
-        memory = 30.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_BaseRecalibrator_GATK {
-        cpus = 1
-        memory = 500.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_ApplyBQSR_GATK {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 4
-            }
-        }
-    }
-    withName: run_MergeSamFiles_Picard {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: deduplicate_records_SAMtools {
-        cpus = 2
-        memory = 8.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_index_SAMtools {
-        cpus = 1
-        memory = 2.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_GetPileupSummaries_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_CalculateContamination_GATK {
-        cpus = 1
-        memory = 5.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-    withName: run_DepthOfCoverage_GATK {
-        cpus = 1
-        memory = 10.GB
-        retry_strategy {
-            memory {
-                strategy = 'exponential'
-                operand = 2
-            }
-        }
-    }
-}

From 87cca2f7b4f88d719b196dcff3460e716da3ba56 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Fri, 15 Nov 2024 10:13:38 -0800
Subject: [PATCH 03/11] Replace old calls with handle_resources()

---
 config/methods.config | 17 +----------------
 1 file changed, 1 insertion(+), 16 deletions(-)

diff --git a/config/methods.config b/config/methods.config
index 1bee57d..e2b8c96 100644
--- a/config/methods.config
+++ b/config/methods.config
@@ -57,7 +57,7 @@ methods {
 
     set_allocation = {
         // Set base and node-specific allocations
-        methods.set_resources_allocation()
+        resource_handler.handle_resources("${projectDir}/config/resources.json")
 
         def node_memory_GB = SysHelper.getAvailMemory().toGiga()
 
@@ -93,19 +93,6 @@ methods {
         }
     }
 
-    modify_base_allocations = {
-        if (!(params.containsKey('base_resource_update') && params.base_resource_update)) {
-            return
-        }
-
-        params.base_resource_update.each { resource, updates ->
-            updates.each { processes, multiplier ->
-                def processes_to_update = (custom_schema_types.is_string(processes)) ? [processes] : processes
-                methods.update_base_resource_allocation(resource, multiplier, processes_to_update)
-            }
-        }
-    }
-
     set_recal_tables = {
         params.use_recal_tables = params.input.containsKey('recalibration_table')
 
@@ -120,13 +107,11 @@ methods {
         schema.validate()
         methods.set_ids_from_bams()
         methods.set_allocation()
-        methods.modify_base_allocations()
         methods.set_log_output_dir()
         methods.set_output_dir()
         methods.set_pipeline_logs()
         methods.set_process()
         methods.detect_mode()
-        retry.setup_retry()
         methods.setup_docker_cpus()
         methods.verify_input_deletion()
         methods.set_recal_tables()

From 41b1da0675c8ef05328f89962f0efc78d58c69df Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Fri, 15 Nov 2024 10:23:48 -0800
Subject: [PATCH 04/11] Update submodule, update import

---
 config/methods.config             | 2 +-
 external/pipeline-Nextflow-config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/methods.config b/config/methods.config
index e2b8c96..5388120 100644
--- a/config/methods.config
+++ b/config/methods.config
@@ -3,7 +3,7 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/csv/csv_pa
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/bam/bam_parser.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/methods/common_methods.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/schema/schema.config"
-includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/retry/retry.config"
+includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/resource_handler/resource_handler.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/store_object_as_json/store_object_as_json.config"
 
 methods {
diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
index a4e99e0..c612346 160000
--- a/external/pipeline-Nextflow-config
+++ b/external/pipeline-Nextflow-config
@@ -1 +1 @@
-Subproject commit a4e99e0260578dbcdee432562f985f47a8100463
+Subproject commit c612346db4dc50972b18ba22908c58bfd8fb391f

From 3276312e4f5fe36a3840e520675788d2a6376ae7 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Fri, 15 Nov 2024 11:13:09 -0800
Subject: [PATCH 05/11] Update CHANGELOG

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 599135d..ab4b10d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### Changed
+
+- Update to branch of `pipeline-Nextflow-config`
+- Replace node-specific configs with computed `resources.json` file
+- Use `resource_handler.handle_resources()`
+
 ## [1.0.2] - 2024-10-08
 
 ### Added

From de53e00018b909534089b65e8bf98e956d15add3 Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Wed, 27 Nov 2024 12:48:14 -0800
Subject: [PATCH 06/11] Update allocation function for custom allocations

---
 config/methods.config | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/config/methods.config b/config/methods.config
index 5388120..c89c78c 100644
--- a/config/methods.config
+++ b/config/methods.config
@@ -56,9 +56,6 @@ methods {
     }
 
     set_allocation = {
-        // Set base and node-specific allocations
-        resource_handler.handle_resources("${projectDir}/config/resources.json")
-
         def node_memory_GB = SysHelper.getAvailMemory().toGiga()
 
         def num_samples = params.samples_to_process.size()
@@ -66,6 +63,8 @@ methods {
         // Divide memory per sample, with a minimum of 20% of total memory
         def mem_to_allocate = Math.max(node_memory_GB * 0.2, (node_memory_GB * 0.9) / num_samples)
 
+        Map custom_allocations = [:]
+
         def processes_to_parallelize_per_sample = [
             'run_BaseRecalibrator_GATK',
             'run_MergeSamFiles_Picard',
@@ -79,12 +78,17 @@ methods {
         ]
 
         processes_to_parallelize_per_sample.each { p ->
-            process["withName:${p}"].memory = "${ mem_to_allocate } GB" as nextflow.util.MemoryUnit
+            custom_allocations[p] = [:]
+            custom_allocations[p]['memory'] = "${ mem_to_allocate } GB" as nextflow.util.MemoryUnit
         }
 
         processes_to_parallelize_per_half_sample.each { p ->
-            process["withName:${p}"].memory = "${ mem_to_allocate / 2 } GB" as nextflow.util.MemoryUnit
+            custom_allocations[p] = [:]
+            custom_allocations[p]['memory'] = "${ mem_to_allocate / 2 } GB" as nextflow.util.MemoryUnit
         }
+
+        // Set base and node-specific allocations
+        resource_handler.handle_resources("${projectDir}/config/resources.json", custom_allocations)
     }
 
     verify_input_deletion = {

From e6b95c4c3432173b1796c4d231fbba780567360e Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Wed, 27 Nov 2024 12:48:39 -0800
Subject: [PATCH 07/11] Update config submodule

---
 external/pipeline-Nextflow-config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
index c612346..f47ee5c 160000
--- a/external/pipeline-Nextflow-config
+++ b/external/pipeline-Nextflow-config
@@ -1 +1 @@
-Subproject commit c612346db4dc50972b18ba22908c58bfd8fb391f
+Subproject commit f47ee5c0a5b2f36f7f71dd268892eaf98da63666

From 19aeebabcd5e5d29125997c9ec06bf16461c6278 Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Mon, 2 Dec 2024 10:07:02 -0800
Subject: [PATCH 08/11] Update config submodule

---
 external/pipeline-Nextflow-config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
index f47ee5c..92d543e 160000
--- a/external/pipeline-Nextflow-config
+++ b/external/pipeline-Nextflow-config
@@ -1 +1 @@
-Subproject commit f47ee5c0a5b2f36f7f71dd268892eaf98da63666
+Subproject commit 92d543e18ca25b70547beb66ec631816354f0983

From e475464f5156b6cce8f1ac8b6a0d459f047ff54c Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Mon, 2 Dec 2024 10:11:55 -0800
Subject: [PATCH 09/11] Update configtests

---
 test/configtest-F16.json | 206 ++++++++++++++++++++-------------------
 test/configtest-F32.json | 206 ++++++++++++++++++++-------------------
 2 files changed, 216 insertions(+), 196 deletions(-)

diff --git a/test/configtest-F16.json b/test/configtest-F16.json
index e86a9fc..e763202 100644
--- a/test/configtest-F16.json
+++ b/test/configtest-F16.json
@@ -51,6 +51,72 @@
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
+      "base_allocations": {
+        "deduplicate_records_SAMtools": {
+          "cpus": "2",
+          "memory": "27.9 GB"
+        },
+        "extract_GenomeIntervals": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_intermediate_files": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_merged_BAM": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_unmerged_BAMs": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "run_ApplyBQSR_GATK": {
+          "cpus": "1",
+          "memory": "2 GB"
+        },
+        "run_BaseRecalibrator_GATK": {
+          "cpus": "1",
+          "memory": "27.9 GB"
+        },
+        "run_CalculateContamination_GATK": {
+          "cpus": "1",
+          "memory": "14 GB"
+        },
+        "run_DepthOfCoverage_GATK": {
+          "cpus": "1",
+          "memory": "14 GB"
+        },
+        "run_GetPileupSummaries_GATK": {
+          "cpus": "1",
+          "memory": "14 GB"
+        },
+        "run_IndelRealigner_GATK": {
+          "cpus": "2",
+          "memory": "4 GB"
+        },
+        "run_MergeSamFiles_Picard": {
+          "cpus": "2",
+          "memory": "27.9 GB"
+        },
+        "run_RealignerTargetCreator_GATK": {
+          "cpus": "2",
+          "memory": "4 GB"
+        },
+        "run_SplitIntervals_GATK": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "run_index_SAMtools": {
+          "cpus": "1",
+          "memory": "2 GB"
+        },
+        "run_validate_PipeVal": {
+          "cpus": "1",
+          "memory": "1 GB"
+        }
+      },
       "blcds_registered_dataset": false,
       "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz",
       "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi",
@@ -89,6 +155,7 @@
       "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z",
       "max_cpus": "16",
       "max_memory": "31 GB",
+      "max_time": "24d 20h 31m 24s",
       "metapipeline_delete_input_bams": false,
       "metapipeline_states_to_delete": [
         "normal",
@@ -96,141 +163,78 @@
       ],
       "min_cpus": "1",
       "min_memory": "1 MB",
+      "min_time": "1s",
       "output_dir": "/tmp/outputs",
       "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
       "pipeval_version": "4.0.0-rc.2",
-      "proc_resource_params": {
+      "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
+      "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
+      "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
+      "retry_information": {
         "deduplicate_records_SAMtools": {
-          "cpus": "2",
-          "memory": "27.9 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
-        "extract_GenomeIntervals": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_intermediate_files": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_merged_BAM": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_unmerged_BAMs": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
         "run_ApplyBQSR_GATK": {
-          "cpus": "1",
-          "memory": "2 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "4",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "4",
+            "strategy": "exponential"
           }
         },
         "run_BaseRecalibrator_GATK": {
-          "cpus": "1",
-          "memory": "27.9 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_CalculateContamination_GATK": {
-          "cpus": "1",
-          "memory": "14 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_DepthOfCoverage_GATK": {
-          "cpus": "1",
-          "memory": "14 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_GetPileupSummaries_GATK": {
-          "cpus": "1",
-          "memory": "14 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_IndelRealigner_GATK": {
-          "cpus": "2",
-          "memory": "4 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "4",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "4",
+            "strategy": "exponential"
           }
         },
         "run_MergeSamFiles_Picard": {
-          "cpus": "2",
-          "memory": "27.9 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_RealignerTargetCreator_GATK": {
-          "cpus": "2",
-          "memory": "4 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
-        "run_SplitIntervals_GATK": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
         "run_index_SAMtools": {
-          "cpus": "1",
-          "memory": "2 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
-        },
-        "run_validate_PipeVal": {
-          "cpus": "1",
-          "memory": "1 GB"
         }
       },
-      "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
-      "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
-      "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
       "samples_to_process": [
         {
           "id": "4915723",
@@ -451,6 +455,12 @@
       "enabled": true,
       "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
     },
+    "resource_handler": {
+      "handle_resources": "closure()",
+      "set_resource_limit_params": "closure()",
+      "set_retry": "closure()",
+      "setup_retry": "closure()"
+    },
     "timeline": {
       "enabled": true,
       "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
diff --git a/test/configtest-F32.json b/test/configtest-F32.json
index c25b5da..0ea94bc 100644
--- a/test/configtest-F32.json
+++ b/test/configtest-F32.json
@@ -51,6 +51,72 @@
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
+      "base_allocations": {
+        "deduplicate_records_SAMtools": {
+          "cpus": "2",
+          "memory": "57.6 GB"
+        },
+        "extract_GenomeIntervals": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_intermediate_files": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_merged_BAM": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "remove_unmerged_BAMs": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "run_ApplyBQSR_GATK": {
+          "cpus": "1",
+          "memory": "2 GB"
+        },
+        "run_BaseRecalibrator_GATK": {
+          "cpus": "1",
+          "memory": "57.6 GB"
+        },
+        "run_CalculateContamination_GATK": {
+          "cpus": "1",
+          "memory": "28.8 GB"
+        },
+        "run_DepthOfCoverage_GATK": {
+          "cpus": "1",
+          "memory": "28.8 GB"
+        },
+        "run_GetPileupSummaries_GATK": {
+          "cpus": "1",
+          "memory": "28.8 GB"
+        },
+        "run_IndelRealigner_GATK": {
+          "cpus": "4",
+          "memory": "6 GB"
+        },
+        "run_MergeSamFiles_Picard": {
+          "cpus": "2",
+          "memory": "57.6 GB"
+        },
+        "run_RealignerTargetCreator_GATK": {
+          "cpus": "4",
+          "memory": "6 GB"
+        },
+        "run_SplitIntervals_GATK": {
+          "cpus": "1",
+          "memory": "1 GB"
+        },
+        "run_index_SAMtools": {
+          "cpus": "1",
+          "memory": "2 GB"
+        },
+        "run_validate_PipeVal": {
+          "cpus": "1",
+          "memory": "1 GB"
+        }
+      },
       "blcds_registered_dataset": false,
       "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz",
       "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi",
@@ -89,6 +155,7 @@
       "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z",
       "max_cpus": "32",
       "max_memory": "64 GB",
+      "max_time": "24d 20h 31m 24s",
       "metapipeline_delete_input_bams": false,
       "metapipeline_states_to_delete": [
         "normal",
@@ -96,141 +163,78 @@
       ],
       "min_cpus": "1",
       "min_memory": "1 MB",
+      "min_time": "1s",
       "output_dir": "/tmp/outputs",
       "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
       "pipeval_version": "4.0.0-rc.2",
-      "proc_resource_params": {
+      "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
+      "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
+      "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
+      "retry_information": {
         "deduplicate_records_SAMtools": {
-          "cpus": "2",
-          "memory": "57.6 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
-        "extract_GenomeIntervals": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_intermediate_files": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_merged_BAM": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
-        "remove_unmerged_BAMs": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
         "run_ApplyBQSR_GATK": {
-          "cpus": "1",
-          "memory": "2 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "4",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "4",
+            "strategy": "exponential"
           }
         },
         "run_BaseRecalibrator_GATK": {
-          "cpus": "1",
-          "memory": "57.6 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_CalculateContamination_GATK": {
-          "cpus": "1",
-          "memory": "28.8 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_DepthOfCoverage_GATK": {
-          "cpus": "1",
-          "memory": "28.8 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_GetPileupSummaries_GATK": {
-          "cpus": "1",
-          "memory": "28.8 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_IndelRealigner_GATK": {
-          "cpus": "4",
-          "memory": "6 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "4",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "4",
+            "strategy": "exponential"
           }
         },
         "run_MergeSamFiles_Picard": {
-          "cpus": "2",
-          "memory": "57.6 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
         "run_RealignerTargetCreator_GATK": {
-          "cpus": "4",
-          "memory": "6 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
         },
-        "run_SplitIntervals_GATK": {
-          "cpus": "1",
-          "memory": "1 GB"
-        },
         "run_index_SAMtools": {
-          "cpus": "1",
-          "memory": "2 GB",
-          "retry_strategy": {
-            "memory": {
-              "operand": "2",
-              "strategy": "exponential"
-            }
+          "memory": {
+            "operand": "2",
+            "strategy": "exponential"
           }
-        },
-        "run_validate_PipeVal": {
-          "cpus": "1",
-          "memory": "1 GB"
         }
       },
-      "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
-      "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
-      "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
       "samples_to_process": [
         {
           "id": "4915723",
@@ -451,6 +455,12 @@
       "enabled": true,
       "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
     },
+    "resource_handler": {
+      "handle_resources": "closure()",
+      "set_resource_limit_params": "closure()",
+      "set_retry": "closure()",
+      "setup_retry": "closure()"
+    },
     "timeline": {
       "enabled": true,
       "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"

From c5b6c6ffe3bfa031574db875ea099373c4de8ad7 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Wed, 18 Dec 2024 09:40:45 -0800
Subject: [PATCH 10/11] Update submodule

---
 external/pipeline-Nextflow-config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
index 92d543e..07c99b8 160000
--- a/external/pipeline-Nextflow-config
+++ b/external/pipeline-Nextflow-config
@@ -1 +1 @@
-Subproject commit 92d543e18ca25b70547beb66ec631816354f0983
+Subproject commit 07c99b8d93f4232147546302bcae2bdb2a346705

From 9125ad6b18ebee1cf53c8f098900531052b8615c Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Thu, 19 Dec 2024 17:37:39 -0800
Subject: [PATCH 11/11] Adjust default resources with min and maxes

---
 config/resources.json | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/config/resources.json b/config/resources.json
index f4959d1..cf87a61 100644
--- a/config/resources.json
+++ b/config/resources.json
@@ -1056,13 +1056,13 @@
         },
         "run_RealignerTargetCreator_GATK": {
             "cpus": {
-                "min": 6,
-                "fraction": 0.08,
+                "min": 2,
+                "fraction": 0.10,
                 "max": 6
             },
             "memory": {
-                "min": "10 GB",
-                "fraction": 0.07,
+                "min": "4 GB",
+                "fraction": 0.10,
                 "max": "10 GB"
             },
             "retry_strategy": {
@@ -1074,13 +1074,13 @@
         },
         "run_IndelRealigner_GATK": {
             "cpus": {
-                "min": 6,
-                "fraction": 0.08,
+                "min": 2,
+                "fraction": 0.10,
                 "max": 6
             },
             "memory": {
-                "min": "10 GB",
-                "fraction": 0.07,
+                "min": "4 GB",
+                "fraction": 0.10,
                 "max": "10 GB"
             },
             "retry_strategy": {
@@ -1097,7 +1097,7 @@
                 "max": 1
             },
             "memory": {
-                "min": "72 GB",
+                "min": "1 GB",
                 "fraction": 0.53,
                 "max": "72 GB"
             },
@@ -1133,8 +1133,8 @@
                 "max": 2
             },
             "memory": {
-                "min": "8 GB",
-                "fraction": 0.06,
+                "min": "4 GB",
+                "fraction": 0.10,
                 "max": "8 GB"
             },
             "retry_strategy": {
@@ -1151,8 +1151,8 @@
                 "max": 2
             },
             "memory": {
-                "min": "8 GB",
-                "fraction": 0.06,
+                "min": "4 GB",
+                "fraction": 0.10,
                 "max": "8 GB"
             },
             "retry_strategy": {
@@ -1187,9 +1187,9 @@
                 "max": 1
             },
             "memory": {
-                "min": "5 GB",
-                "fraction": 0.04,
-                "max": "5 GB"
+                "min": "3 GB",
+                "fraction": 0.05,
+                "max": "10 GB"
             },
             "retry_strategy": {
                 "memory": {
@@ -1205,9 +1205,9 @@
                 "max": 1
             },
             "memory": {
-                "min": "5 GB",
-                "fraction": 0.04,
-                "max": "5 GB"
+                "min": "3 GB",
+                "fraction": 0.05,
+                "max": "10 GB"
             },
             "retry_strategy": {
                 "memory": {
@@ -1223,8 +1223,8 @@
                 "max": 1
             },
             "memory": {
-                "min": "10 GB",
-                "fraction": 0.07,
+                "min": "4 GB",
+                "fraction": 0.10,
                 "max": "10 GB"
             },
             "retry_strategy": {