Bump external/pipeline-Nextflow-config from 3ec7186 to f3448ac (#145

) * Bump external/pipeline-Nextflow-config from `3ec7186` to `f3448ac` Bumps [external/pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config) from `3ec7186` to `f3448ac`. - [Release notes](https://github.com/uclahs-cds/pipeline-Nextflow-config/releases) - [Commits](uclahs-cds/pipeline-Nextflow-config@3ec7186...f3448ac) --- updated-dependencies: - dependency-name: external/pipeline-Nextflow-config dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Update expected test changes --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
uclahs-cds · Mar 22, 2024 · 9ba216b · 9ba216b
1 parent 49aeb74
commit 9ba216b
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diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -146,98 +146,6 @@
       "verbose": false,
       "work_dir": "/scratch/523557"
     },
-    "params_schema": {
-      "algorithm": {
-        "choices": [
-          "delly",
-          "manta"
-        ],
-        "default": [
-          "delly",
-          "manta"
-        ],
-        "help": "List of available somatic SV callers",
-        "required": true,
-        "type": "List"
-      },
-      "dataset_id": {
-        "help": "Dataset identifier",
-        "required": true,
-        "type": "String"
-      },
-      "exclusion_file": {
-        "help": "Absoulte path to an exclusion file",
-        "mode": "r",
-        "required": true,
-        "type": "Path"
-      },
-      "filter_condition": {
-        "default": "FILTER=\\='PASS'",
-        "help": "",
-        "required": true,
-        "type": "String"
-      },
-      "input": {
-        "elements": {
-          "BAM": {
-            "elements": {
-              "normal": {
-                "help": "Input normal BAMs",
-                "required": false,
-                "type": "BAMEntryList"
-              },
-              "tumor": {
-                "help": "Input tumor BAMs",
-                "required": false,
-                "type": "BAMEntryList"
-              }
-            },
-            "help": "Input BAMs for somatic structural variant calling",
-            "required": true,
-            "type": "InputBAMNamespace"
-          }
-        },
-        "help": "Input samples",
-        "required": true,
-        "type": "InputNamespace"
-      },
-      "mad_cutoff": {
-        "default": "15",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "map_qual": {
-        "default": "20",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "min_clique_size": {
-        "default": "5",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "output_dir": {
-        "help": "Absolute path to output directory",
-        "mode": "w",
-        "required": true,
-        "type": "Path"
-      },
-      "reference_fasta": {
-        "help": "Absolute path to a reference FASTA file",
-        "mode": "r",
-        "required": true,
-        "type": "Path"
-      },
-      "sample_id": {
-        "help": "Sample ID",
-        "required": true,
-        "type": "String"
-      }
-    },
-    "proc_names": "[Ljava.lang.String;@dec0ded",
     "process": {
       "cache": false,
       "commonRetryCodes": [
@@ -374,97 +282,6 @@
       "file": "/tmp/outputs/call-sSV-6.1.0/610093/log-call-sSV-6.1.0-19970704T165655Z/nextflow-log/trace.txt"
     },
     "tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]",
-    "workDir": "/scratch/523557",
-    "yaml": {
-      "algorithm": {
-        "choices": [
-          "delly",
-          "manta"
-        ],
-        "default": [
-          "delly",
-          "manta"
-        ],
-        "help": "List of available somatic SV callers",
-        "required": true,
-        "type": "List"
-      },
-      "dataset_id": {
-        "help": "Dataset identifier",
-        "required": true,
-        "type": "String"
-      },
-      "exclusion_file": {
-        "help": "Absoulte path to an exclusion file",
-        "mode": "r",
-        "required": true,
-        "type": "Path"
-      },
-      "filter_condition": {
-        "default": "FILTER=\\='PASS'",
-        "help": "",
-        "required": true,
-        "type": "String"
-      },
-      "input": {
-        "elements": {
-          "BAM": {
-            "elements": {
-              "normal": {
-                "help": "Input normal BAMs",
-                "required": false,
-                "type": "BAMEntryList"
-              },
-              "tumor": {
-                "help": "Input tumor BAMs",
-                "required": false,
-                "type": "BAMEntryList"
-              }
-            },
-            "help": "Input BAMs for somatic structural variant calling",
-            "required": true,
-            "type": "InputBAMNamespace"
-          }
-        },
-        "help": "Input samples",
-        "required": true,
-        "type": "InputNamespace"
-      },
-      "mad_cutoff": {
-        "default": "15",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "map_qual": {
-        "default": "20",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "min_clique_size": {
-        "default": "5",
-        "help": "",
-        "required": true,
-        "type": "Integer"
-      },
-      "output_dir": {
-        "help": "Absolute path to output directory",
-        "mode": "w",
-        "required": true,
-        "type": "Path"
-      },
-      "reference_fasta": {
-        "help": "Absolute path to a reference FASTA file",
-        "mode": "r",
-        "required": true,
-        "type": "Path"
-      },
-      "sample_id": {
-        "help": "Sample ID",
-        "required": true,
-        "type": "String"
-      }
-    }
+    "workDir": "/scratch/523557"
   }
 }