diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga
index 90391a239..f68fbb603 100644
--- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga
+++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.3",
+    "release": "0.4",
     "name": "Assembly-Hifi-Trio-phasing-VGP5",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=merqury_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -1178,7 +1178,7 @@
         },
         "30": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 30,
             "input_connections": {
@@ -1220,15 +1220,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "ae31efe9-7f56-4a2d-b811-d77d4f8b0abf",
             "when": null,
@@ -1242,7 +1242,7 @@
         },
         "31": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 31,
             "input_connections": {
@@ -1284,15 +1284,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "f2a02b12-43b7-4969-a999-dbc18b820c2f",
             "when": null,
@@ -1359,7 +1359,7 @@
         },
         "33": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 33,
             "input_connections": {
@@ -1415,15 +1415,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "653200d3-c548-4dd2-87cb-e8b40fbc8235",
             "when": null,
@@ -1437,7 +1437,7 @@
         },
         "34": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 34,
             "input_connections": {
@@ -1493,15 +1493,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "77c35546-0668-45d5-aa10-2c5048fd4256",
             "when": null,
@@ -1515,7 +1515,7 @@
         },
         "35": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 35,
             "input_connections": {
@@ -1546,15 +1546,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "fb185c69-e1a1-47a4-b983-d25d94f25522",
             "when": null,
@@ -1562,7 +1562,7 @@
         },
         "36": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 36,
             "input_connections": {
@@ -1593,15 +1593,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "a3de4200-b7d2-4cd5-bcca-fa6f548ed6a0",
             "when": null,
@@ -1609,7 +1609,7 @@
         },
         "37": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 37,
             "input_connections": {
@@ -1644,15 +1644,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "60492710-1411-45ff-abe6-1c94644bcca4",
             "when": null,
@@ -1660,7 +1660,7 @@
         },
         "38": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "errors": null,
             "id": 38,
             "input_connections": {
@@ -1695,15 +1695,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "f4a3eff8ab85",
+                "changeset_revision": "764f2516d837",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.9+galaxy0",
+            "tool_version": "1.3.9+galaxy1",
             "type": "tool",
             "uuid": "904feec3-140a-4aff-a8af-29592733175e",
             "when": null,
@@ -1801,7 +1801,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "5.8.0+galaxy0",
             "type": "tool",
             "uuid": "bc06da8e-e5cb-493e-98d1-c974a3e46cff",
@@ -1916,7 +1916,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "5.8.0+galaxy0",
             "type": "tool",
             "uuid": "4931c626-b636-43c3-b19b-3c778199b9a8",
@@ -2467,7 +2467,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "0db8092c-fa2f-4780-97e9-eddf9381a024"
+                "uuid": "857e24f8-fb7a-4a3f-a55c-aea22e32a282"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -2849,7 +2849,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "89293c64-2b08-41e3-912f-e3c226047551"
+                "uuid": "cd145237-3c4a-400d-90d4-9603f3098ce6"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -3741,7 +3741,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "b78e621c-7220-413c-bf73-7109f9bd1e62"
+                "uuid": "37bb5ce3-a485-4340-b37a-7f3ab5c655fa"
             },
             "tool_id": null,
             "type": "subworkflow",
diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md
index bdeb6cb38..17d779188 100644
--- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md
+++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.4] 2024-12-16
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1`
+
 ## [0.3] 2024-11-11
 
 ### Automatic update