diff --git a/.github/workflows/wftest.yml b/.github/workflows/wftest.yml
index 1344d7a..b0e927d 100644
--- a/.github/workflows/wftest.yml
+++ b/.github/workflows/wftest.yml
@@ -10,7 +10,7 @@ jobs:
     with:
       python-version-list: "[\"3.7\"]"
       galaxy-fork: galaxyproject
-      galaxy-branch: release_23.1
+      galaxy-branch: release_23.2
   test:
     name: Test workflow
     needs: setup
@@ -19,6 +19,6 @@ jobs:
       galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
       python-version-list: "[\"3.7\"]"
       galaxy-fork: galaxyproject
-      galaxy-branch: release_23.1
+      galaxy-branch: release_23.2
       repository-list: '.'
       check-outputs: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ea69c8..66826ae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.4.2] 2024-03-06
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3`
+
 ## [0.4.1] 2023-11-20
 
 - Fix author in dockstore
diff --git a/consensus-from-variation.ga b/consensus-from-variation.ga
index 5714e03..7d19751 100644
--- a/consensus-from-variation.ga
+++ b/consensus-from-variation.ga
@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: consensus construction",
-    "release": "0.4.1",
+    "release": "0.4.2",
     "steps": {
         "0": {
             "annotation": "Collection of VCFs produced by upstream workflows for variation analysis",
@@ -29,14 +29,15 @@
             "name": "Input dataset collection",
             "outputs": [],
             "position": {
-                "left": 348.04998779296875,
-                "top": 524.63330078125
+                "left": 0.0,
+                "top": 306.13330078125
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37",
+            "when": null,
             "workflow_outputs": []
         },
         "1": {
@@ -55,14 +56,15 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 348.5,
-                "top": 687.5
+                "left": 0.45001220703125,
+                "top": 469.0
             },
             "tool_id": null,
             "tool_state": "{\"default\": 0.75, \"parameter_type\": \"float\", \"optional\": true}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "consensus_af_threshold",
@@ -87,14 +89,15 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 348.5,
-                "top": 859.1500244140625
+                "left": 0.45001220703125,
+                "top": 640.6500244140625
             },
             "tool_id": null,
             "tool_state": "{\"default\": 0.25, \"parameter_type\": \"float\", \"optional\": true}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "a2a15cce-94ec-4a76-a3ff-3ea898e9c678",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "non_consensus_af_threshold",
@@ -119,14 +122,15 @@
             "name": "Input dataset collection",
             "outputs": [],
             "position": {
-                "left": 929.36669921875,
-                "top": 613.6666870117188
+                "left": 581.3167114257812,
+                "top": 395.16668701171875
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": null, \"collection_type\": \"list\"}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "23ae69ea-f9a7-4d5f-85f5-63b9d2bd2c50",
+            "when": null,
             "workflow_outputs": []
         },
         "4": {
@@ -145,14 +149,15 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 933.2999877929688,
-                "top": 776.3499755859375
+                "left": 585.25,
+                "top": 557.8499755859375
             },
             "tool_id": null,
             "tool_state": "{\"default\": 5, \"parameter_type\": \"integer\", \"optional\": true}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "cfdc65b0-8393-4ee3-9e27-16b23135fbec",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "depth_threshold",
@@ -177,14 +182,15 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 2631.86669921875,
-                "top": 564.6500244140625
+                "left": 2283.8167114257812,
+                "top": 346.1500244140625
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false}",
+            "tool_state": "{\"optional\": false, \"tag\": null}",
             "tool_version": null,
             "type": "data_input",
             "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214",
+            "when": null,
             "workflow_outputs": []
         },
         "6": {
@@ -208,8 +214,8 @@
                 }
             ],
             "position": {
-                "left": 630.8499755859375,
-                "top": 503.8500061035156
+                "left": 282.79998779296875,
+                "top": 285.3500061035156
             },
             "post_job_actions": {
                 "HideDatasetActionout1": {
@@ -229,6 +235,7 @@
             "tool_version": "0.1.1",
             "type": "tool",
             "uuid": "8ec54933-36d6-404c-b0a6-5a14b04eb30e",
+            "when": null,
             "workflow_outputs": []
         },
         "7": {
@@ -256,8 +263,8 @@
                 }
             ],
             "position": {
-                "left": 581.0499877929688,
-                "top": 1020.5166625976562
+                "left": 233.0,
+                "top": 802.0166625976562
             },
             "post_job_actions": {
                 "HideDatasetActionout1": {
@@ -277,11 +284,12 @@
             "tool_version": "0.1.1",
             "type": "tool",
             "uuid": "51ac3588-c801-4551-8345-b04cc3571fea",
+            "when": null,
             "workflow_outputs": []
         },
         "8": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -290,7 +298,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool bedtools Genome Coverage",
+                    "name": "input_type"
+                }
+            ],
             "label": null,
             "name": "bedtools Genome Coverage",
             "outputs": [
@@ -300,8 +313,8 @@
                 }
             ],
             "position": {
-                "left": 1228.8499755859375,
-                "top": 621.8499755859375
+                "left": 880.7999877929688,
+                "top": 403.3499755859375
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -312,17 +325,18 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
             "tool_shed_repository": {
-                "changeset_revision": "0a5c785ac6db",
+                "changeset_revision": "a1a923cd89e8",
                 "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": "2.29.2",
+            "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",
             "type": "tool",
             "uuid": "d89684f5-5a49-4b4c-821b-6c8a87f3a46e",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "coverage_depth",
@@ -352,8 +366,8 @@
                 }
             ],
             "position": {
-                "left": 1227.36669921875,
-                "top": 778.3499755859375
+                "left": 879.3167114257812,
+                "top": 559.8499755859375
             },
             "post_job_actions": {
                 "HideDatasetActionout1": {
@@ -373,6 +387,7 @@
             "tool_version": "0.1.1",
             "type": "tool",
             "uuid": "089b2659-d4c8-44c8-9ecc-ffe71676e650",
+            "when": null,
             "workflow_outputs": []
         },
         "10": {
@@ -390,7 +405,16 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SnpSift Filter",
+                    "name": "filter_expression"
+                },
+                {
+                    "description": "runtime parameter for tool SnpSift Filter",
+                    "name": "input"
+                }
+            ],
             "label": null,
             "name": "SnpSift Filter",
             "outputs": [
@@ -400,8 +424,8 @@
                 }
             ],
             "position": {
-                "left": 833.3333129882812,
-                "top": 218.5
+                "left": 485.2833251953125,
+                "top": 0.0
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -419,10 +443,11 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.3+t.galaxy1",
             "type": "tool",
             "uuid": "3673b687-1ba0-42f2-ba13-fa3130462079",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "consensus_variants",
@@ -446,7 +471,16 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SnpSift Filter",
+                    "name": "filter_expression"
+                },
+                {
+                    "description": "runtime parameter for tool SnpSift Filter",
+                    "name": "input"
+                }
+            ],
             "label": null,
             "name": "SnpSift Filter",
             "outputs": [
@@ -456,8 +490,8 @@
                 }
             ],
             "position": {
-                "left": 804.7166748046875,
-                "top": 951.8499755859375
+                "left": 456.66668701171875,
+                "top": 733.3499755859375
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -475,10 +509,11 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.3+t.galaxy1",
             "type": "tool",
             "uuid": "fb232cba-e3b2-43f9-bb1f-a9ebc69c9b97",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "filter_failed_variants",
@@ -502,7 +537,16 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Filter",
+                    "name": "cond"
+                },
+                {
+                    "description": "runtime parameter for tool Filter",
+                    "name": "input"
+                }
+            ],
             "label": null,
             "name": "Filter",
             "outputs": [
@@ -512,8 +556,8 @@
                 }
             ],
             "position": {
-                "left": 1561.88330078125,
-                "top": 645.8499755859375
+                "left": 1213.8333129882812,
+                "top": 427.3499755859375
             },
             "post_job_actions": {
                 "RenameDatasetActionout_file1": {
@@ -529,6 +573,7 @@
             "tool_version": "1.1.1",
             "type": "tool",
             "uuid": "8ac27ee3-9e9e-4d6f-b424-2c21f80c87ef",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "low_cov_regions",
@@ -548,7 +593,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SnpSift Extract Fields",
+                    "name": "input"
+                }
+            ],
             "label": null,
             "name": "SnpSift Extract Fields",
             "outputs": [
@@ -558,8 +608,8 @@
                 }
             ],
             "position": {
-                "left": 1155.5,
-                "top": 401.5
+                "left": 807.4500122070312,
+                "top": 183.0
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -577,10 +627,11 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"empty_text\": \"\", \"extract\": \"CHROM POS REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"empty_text\": \"\", \"extract\": \"CHROM POS REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": false, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.3+t.galaxy0",
             "type": "tool",
             "uuid": "5aca2952-a87c-4c77-a259-a22daceab557",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "chrom_pos_ref_called_variants",
@@ -600,7 +651,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SnpSift Extract Fields",
+                    "name": "input"
+                }
+            ],
             "label": null,
             "name": "SnpSift Extract Fields",
             "outputs": [
@@ -610,8 +666,8 @@
                 }
             ],
             "position": {
-                "left": 1022,
-                "top": 1117.5
+                "left": 673.9500122070312,
+                "top": 899.0
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -629,10 +685,11 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"empty_text\": \"\", \"extract\": \"CHROM POS REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"empty_text\": \"\", \"extract\": \"CHROM POS REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": false, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.3+t.galaxy0",
             "type": "tool",
             "uuid": "d99d1a1a-24a7-4379-a7d1-1980303ee08a",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "chrom_pos_ref_failed_variants",
@@ -667,8 +724,8 @@
                 }
             ],
             "position": {
-                "left": 1496.183349609375,
-                "top": 468.1499938964844
+                "left": 1148.1333618164062,
+                "top": 249.64999389648438
             },
             "post_job_actions": {
                 "ChangeDatatypeActionout_file1": {
@@ -693,10 +750,11 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"avoid_scientific_notation\": \"false\", \"error_handling\": {\"auto_col_types\": \"false\", \"fail_on_non_existent_columns\": \"true\", \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.0",
             "type": "tool",
             "uuid": "fd260e32-723d-4a22-8d64-4795557f8159",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "called_variant_sites",
@@ -731,8 +789,8 @@
                 }
             ],
             "position": {
-                "left": 1249.6666259765625,
-                "top": 1137.6500244140625
+                "left": 901.6166381835938,
+                "top": 919.1500244140625
             },
             "post_job_actions": {
                 "ChangeDatatypeActionout_file1": {
@@ -757,10 +815,11 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"avoid_scientific_notation\": \"false\", \"error_handling\": {\"auto_col_types\": \"false\", \"fail_on_non_existent_columns\": \"true\", \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.0",
             "type": "tool",
             "uuid": "116e8e99-53ca-4366-a7e1-e3a9fb0bcfc3",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "failed_variant_sites",
@@ -784,7 +843,16 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Concatenate",
+                    "name": "input1"
+                },
+                {
+                    "description": "runtime parameter for tool Concatenate",
+                    "name": "input2"
+                }
+            ],
             "label": null,
             "name": "Concatenate",
             "outputs": [
@@ -794,8 +862,8 @@
                 }
             ],
             "position": {
-                "left": 1816.933349609375,
-                "top": 755.9166870117188
+                "left": 1468.8833618164062,
+                "top": 537.4166870117188
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -808,15 +876,16 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1",
             "tool_shed_repository": {
-                "changeset_revision": "35a89f8cc96e",
+                "changeset_revision": "73ca13a7ec5f",
                 "name": "concat",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"sameformat\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"sameformat\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.1",
             "type": "tool",
             "uuid": "2b7570fb-9ce5-4a9a-863c-e33efbc88912",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "low_cov_regions_plus_filter_failed",
@@ -836,7 +905,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Merge",
+                    "name": "input1"
+                }
+            ],
             "label": null,
             "name": "Merge",
             "outputs": [
@@ -846,8 +920,8 @@
                 }
             ],
             "position": {
-                "left": 2051.36669921875,
-                "top": 752.1666870117188
+                "left": 1703.3167114257812,
+                "top": 533.6666870117188
             },
             "post_job_actions": {
                 "ChangeDatatypeActionoutput": {
@@ -867,15 +941,16 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0",
             "tool_shed_repository": {
-                "changeset_revision": "381cd27bf67a",
+                "changeset_revision": "debffd27642d",
                 "name": "merge",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"returntype\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"returntype\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.0",
             "type": "tool",
             "uuid": "3e63167b-6560-4b6d-a409-7d3707039222",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "low_cov_regions_plus_filter_failed_combined",
@@ -899,7 +974,16 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Subtract",
+                    "name": "input1"
+                },
+                {
+                    "description": "runtime parameter for tool Subtract",
+                    "name": "input2"
+                }
+            ],
             "label": null,
             "name": "Subtract",
             "outputs": [
@@ -909,8 +993,8 @@
                 }
             ],
             "position": {
-                "left": 2307.5166015625,
-                "top": 626.5
+                "left": 1959.4666137695312,
+                "top": 408.0
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -923,7 +1007,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0",
             "tool_shed_repository": {
-                "changeset_revision": "0145969324c4",
+                "changeset_revision": "0427ca314f3d",
                 "name": "subtract",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -932,6 +1016,7 @@
             "tool_version": "1.0.0",
             "type": "tool",
             "uuid": "51b26960-4ee7-4a3d-96cb-a6b3950c173e",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "masking_regions",
@@ -966,8 +1051,8 @@
                 }
             ],
             "position": {
-                "left": 2492.88330078125,
-                "top": 804.1666870117188
+                "left": 2144.8333129882812,
+                "top": 585.6666870117188
             },
             "post_job_actions": {
                 "ChangeDatatypeActionout_file1": {
@@ -992,10 +1077,11 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"avoid_scientific_notation\": \"false\", \"error_handling\": {\"auto_col_types\": \"true\", \"fail_on_non_existent_columns\": \"true\", \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) + 1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) + 1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.0",
             "type": "tool",
             "uuid": "e06fe045-f0f0-4c32-80ad-a8e070946a2f",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "1_based_masking_regions",
@@ -1006,7 +1092,7 @@
         },
         "21": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
             "errors": null,
             "id": 21,
             "input_connections": {
@@ -1023,7 +1109,20 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool bcftools consensus",
+                    "name": "input_file"
+                },
+                {
+                    "description": "runtime parameter for tool bcftools consensus",
+                    "name": "reference_source"
+                },
+                {
+                    "description": "runtime parameter for tool bcftools consensus",
+                    "name": "sec_default"
+                }
+            ],
             "label": null,
             "name": "bcftools consensus",
             "outputs": [
@@ -1033,8 +1132,8 @@
                 }
             ],
             "position": {
-                "left": 2951.88330078125,
-                "top": 462.16668701171875
+                "left": 2603.8333129882812,
+                "top": 243.66668701171875
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput_file": {
@@ -1045,17 +1144,18 @@
                     "output_name": "output_file"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "d3081540d175",
+                "changeset_revision": "147de996e34f",
                 "name": "bcftools_consensus",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"absent\": \"\", \"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.15.1+galaxy2",
+            "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": true, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.15.1+galaxy3",
             "type": "tool",
             "uuid": "698a9a8c-f6fe-430b-a7e0-cf9e1d058d02",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "consensus",
@@ -1075,7 +1175,12 @@
                     "output_name": "output_file"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Collapse Collection",
+                    "name": "input_list"
+                }
+            ],
             "label": null,
             "name": "Collapse Collection",
             "outputs": [
@@ -1085,8 +1190,8 @@
                 }
             ],
             "position": {
-                "left": 3211.550048828125,
-                "top": 486
+                "left": 2863.5000610351562,
+                "top": 267.5
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -1104,10 +1209,11 @@
                 "owner": "nml",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "5.1.0",
             "type": "tool",
             "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "multisample_consensus_fasta",
@@ -1122,4 +1228,4 @@
         "covid19.galaxyproject.org"
     ],
     "uuid": "06dc40a7-99f2-4b3c-ae21-b3dcb239306f"
-}
+}
\ No newline at end of file
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 815e569..6126bf7 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -21,7 +21,7 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "datePublished": "2023-11-23T13:33:07.998349",
+            "datePublished": "2024-03-06T09:35:48.806234",
             "hasPart": [
                 {
                     "@id": "consensus-from-variation.ga"
@@ -72,7 +72,7 @@
                 "@id": "#galaxy"
             },
             "url": "https://github.com/iwc-workflows/sars-cov-2-consensus-from-variation",
-            "version": "0.4.1"
+            "version": "0.4.2"
         },
         {
             "@id": "#galaxy",
@@ -138,7 +138,7 @@
             "conformsTo": {
                 "@id": "https://w3id.org/ro/terms/test#PlanemoEngine"
             },
-            "engineVersion": ">=0.75.18"
+            "engineVersion": ">=0.75.21"
         },
         {
             "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",