From 651faba764133e6d1cd15a3b7a8eb261f6050743 Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Mon, 9 Dec 2024 10:37:23 -0800
Subject: [PATCH] Update configtests

---
 test/configtest-F16.json | 62 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/test/configtest-F16.json b/test/configtest-F16.json
index 0292109..bb7012d 100644
--- a/test/configtest-F16.json
+++ b/test/configtest-F16.json
@@ -66,10 +66,14 @@
       "docker_container_registry": "ghcr.io/uclahs-cds",
       "docker_image_bcftools": "ghcr.io/uclahs-cds/bcftools:1.15.1",
       "docker_image_delly": "ghcr.io/uclahs-cds/delly:1.2.6",
+      "docker_image_gridss": "ghcr.io/uclahs-cds/gridss:2.13.2",
       "docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0",
       "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
       "exclusion_file": "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv",
       "filter_condition": "FILTER=\\='PASS'",
+      "gridss_blacklist": "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed",
+      "gridss_reference_fasta": "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
+      "gridss_version": "2.13.2",
       "input": {
         "BAM": {
           "normal": [
@@ -89,6 +93,7 @@
       "min_clique_size": "5",
       "min_cpus": "1",
       "min_memory": "1 MB",
+      "other_jvm_heap": "4 GB",
       "output_dir": "/tmp/outputs",
       "output_dir_base": "/tmp/outputs/call-sSV-VER.SI.ON/610093",
       "pipeval_version": "4.0.0-rc.2",
@@ -103,6 +108,16 @@
             }
           }
         },
+        "call_sSV_GRIDSS": {
+          "cpus": "8",
+          "memory": "15 GB",
+          "retry_strategy": {
+            "memory": {
+              "operand": "2",
+              "strategy": "exponential"
+            }
+          }
+        },
         "call_sSV_Manta": {
           "cpus": "1",
           "memory": "16 GB",
@@ -123,6 +138,16 @@
             }
           }
         },
+        "preprocess_BAM_GRIDSS": {
+          "cpus": "4",
+          "memory": "10 GB",
+          "retry_strategy": {
+            "memory": {
+              "operand": "2",
+              "strategy": "exponential"
+            }
+          }
+        },
         "query_SampleName_BCFtools": {
           "cpus": "1",
           "memory": "3 GB",
@@ -133,6 +158,16 @@
             }
           }
         },
+        "run_assembly_GRIDSS": {
+          "cpus": "8",
+          "memory": "15 GB",
+          "retry_strategy": {
+            "memory": {
+              "operand": "2",
+              "strategy": "exponential"
+            }
+          }
+        },
         "run_validate_PipeVal": {
           "cpus": "1",
           "memory": "1 GB"
@@ -242,6 +277,15 @@
           "closure": "retry_updater(16 GB, exponential, 2, $task.attempt, memory)"
         }
       },
+      "withName:call_sSV_GRIDSS": {
+        "cpus": "8",
+        "memory": {
+          "1": "15 GB",
+          "2": "30 GB",
+          "3": "31 GB",
+          "closure": "retry_updater(15 GB, exponential, 2, $task.attempt, memory)"
+        }
+      },
       "withName:call_sSV_Manta": {
         "cpus": "1",
         "memory": {
@@ -260,6 +304,15 @@
           "closure": "retry_updater(3 GB, exponential, 2, $task.attempt, memory)"
         }
       },
+      "withName:preprocess_BAM_GRIDSS": {
+        "cpus": "4",
+        "memory": {
+          "1": "10 GB",
+          "2": "20 GB",
+          "3": "31 GB",
+          "closure": "retry_updater(10 GB, exponential, 2, $task.attempt, memory)"
+        }
+      },
       "withName:query_SampleName_BCFtools": {
         "cpus": "1",
         "memory": {
@@ -269,6 +322,15 @@
           "closure": "retry_updater(3 GB, exponential, 2, $task.attempt, memory)"
         }
       },
+      "withName:run_assembly_GRIDSS": {
+        "cpus": "8",
+        "memory": {
+          "1": "15 GB",
+          "2": "30 GB",
+          "3": "31 GB",
+          "closure": "retry_updater(15 GB, exponential, 2, $task.attempt, memory)"
+        }
+      },
       "withName:run_validate_PipeVal": {
         "cpus": "1",
         "memory": "1 GB"