diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md
index 66826ae740..ca2a7299e9 100644
--- a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.4.3] 2024-05-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`
+
 ## [0.4.2] 2024-03-06
 
 ### Automatic update
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
index 7d19751edd..4257dd90e7 100644
--- a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: consensus construction",
-    "release": "0.4.2",
+    "release": "0.4.3",
     "steps": {
         "0": {
             "annotation": "Collection of VCFs produced by upstream workflows for variation analysis",
@@ -289,7 +289,7 @@
         },
         "8": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -325,15 +325,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
             "tool_shed_repository": {
-                "changeset_revision": "a1a923cd89e8",
+                "changeset_revision": "64e2edfe7a2c",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": true, \"scale\": \"1.0\"}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.30.0",
+            "tool_version": "2.31.1",
             "type": "tool",
             "uuid": "d89684f5-5a49-4b4c-821b-6c8a87f3a46e",
             "when": null,
@@ -409,10 +409,6 @@
                 {
                     "description": "runtime parameter for tool SnpSift Filter",
                     "name": "filter_expression"
-                },
-                {
-                    "description": "runtime parameter for tool SnpSift Filter",
-                    "name": "input"
                 }
             ],
             "label": null,
@@ -475,10 +471,6 @@
                 {
                     "description": "runtime parameter for tool SnpSift Filter",
                     "name": "filter_expression"
-                },
-                {
-                    "description": "runtime parameter for tool SnpSift Filter",
-                    "name": "input"
                 }
             ],
             "label": null,
@@ -537,16 +529,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Filter",
-                    "name": "cond"
-                },
-                {
-                    "description": "runtime parameter for tool Filter",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Filter",
             "outputs": [
@@ -593,12 +576,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool SnpSift Extract Fields",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "SnpSift Extract Fields",
             "outputs": [
@@ -651,12 +629,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool SnpSift Extract Fields",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "SnpSift Extract Fields",
             "outputs": [
@@ -709,12 +682,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Compute",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Compute",
             "outputs": [
@@ -774,12 +742,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Compute",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Compute",
             "outputs": [
@@ -843,16 +806,7 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Concatenate",
-                    "name": "input1"
-                },
-                {
-                    "description": "runtime parameter for tool Concatenate",
-                    "name": "input2"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Concatenate",
             "outputs": [
@@ -905,12 +859,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Merge",
-                    "name": "input1"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Merge",
             "outputs": [
@@ -974,16 +923,7 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Subtract",
-                    "name": "input1"
-                },
-                {
-                    "description": "runtime parameter for tool Subtract",
-                    "name": "input2"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Subtract",
             "outputs": [
@@ -1036,12 +976,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Compute",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Compute",
             "outputs": [
@@ -1110,10 +1045,6 @@
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool bcftools consensus",
-                    "name": "input_file"
-                },
                 {
                     "description": "runtime parameter for tool bcftools consensus",
                     "name": "reference_source"
@@ -1175,12 +1106,7 @@
                     "output_name": "output_file"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Collapse Collection",
-                    "name": "input_list"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Collapse Collection",
             "outputs": [