diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
index 6e1a075645..cc4de0856f 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.6.5] - 2026-03-30
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3`
+
 ## [0.6.4] - 2026-01-19
 
 ### Automatic update
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
index 9f875d2a7e..9b62d98a5d 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
@@ -902,7 +902,7 @@
                                 },
                                 "3": {
                                     "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                                     "errors": null,
                                     "id": 3,
                                     "input_connections": {
@@ -931,16 +931,16 @@
                                             "output_name": "output"
                                         }
                                     },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                                     "tool_shed_repository": {
-                                        "changeset_revision": "d3c07d270a50",
+                                        "changeset_revision": "3e27acfa4830",
                                         "name": "collection_element_identifiers",
                                         "owner": "iuc",
                                         "tool_shed": "toolshed.g2.bx.psu.edu"
                                     },
                                     "tool_state": "{\"__input_ext\": \"tsv\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_uuid": null,
-                                    "tool_version": "0.0.2",
+                                    "tool_version": "0.0.3",
                                     "type": "tool",
                                     "uuid": "ff023a14-a401-4ede-8dfb-2187d2d8ad84",
                                     "when": null,
@@ -1329,7 +1329,7 @@
                                 }
                             },
                             "tags": [],
-                            "uuid": "525ae087-0bd6-4e3d-beb1-3cc0f2ecc3bd"
+                            "uuid": "6dc426d7-e144-45e1-a831-e413015a2f82"
                         },
                         "tool_id": null,
                         "type": "subworkflow",
@@ -1345,7 +1345,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "a37fd109-bd3d-4f52-a1f9-4b7bc039f3b5"
+                "uuid": "6cea80d2-dc3d-41e4-86d7-c199e5566103"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1728,7 +1728,7 @@
                     },
                     "3": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
@@ -1757,16 +1757,16 @@
                                 "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "d3c07d270a50",
+                            "changeset_revision": "3e27acfa4830",
                             "name": "collection_element_identifiers",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"__input_ext\": \"tsv\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_uuid": null,
-                        "tool_version": "0.0.2",
+                        "tool_version": "0.0.3",
                         "type": "tool",
                         "uuid": "ff023a14-a401-4ede-8dfb-2187d2d8ad84",
                         "when": null,
@@ -2155,7 +2155,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "cfb78cc9-bbc2-4ca6-a057-9308a7e9d36d"
+                "uuid": "9f4b8285-c140-4afb-9b7f-cf9aaf8e749c"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -2227,7 +2227,7 @@
     "tags": [
         "name:single-cell"
     ],
-    "uuid": "952929c6-9f20-436b-8ead-c153a5133720",
+    "uuid": "501af7ee-f6c2-4d12-8d41-76da87d9f4ff",
     "version": 1,
-    "release": "0.6.4"
+    "release": "0.6.5"
 }
\ No newline at end of file
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
index 3587bcf41b..8d534df433 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
@@ -608,7 +608,7 @@
                     },
                     "3": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
@@ -637,16 +637,16 @@
                                 "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "d3c07d270a50",
+                            "changeset_revision": "3e27acfa4830",
                             "name": "collection_element_identifiers",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"__input_ext\": \"tsv\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_uuid": null,
-                        "tool_version": "0.0.2",
+                        "tool_version": "0.0.3",
                         "type": "tool",
                         "uuid": "ff023a14-a401-4ede-8dfb-2187d2d8ad84",
                         "when": null,
@@ -1035,7 +1035,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "6ee54a42-da56-4e63-b06d-8f09a30d025c"
+                "uuid": "3150821c-909c-4eb8-bb24-7123e5003e0f"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1053,7 +1053,7 @@
     "tags": [
         "name:single-cell"
     ],
-    "uuid": "9a50de06-245a-4498-88da-796a555a8092",
+    "uuid": "0953d007-7038-4f41-b913-db54f3e2b2fe",
     "version": 1,
-    "release": "0.6.4"
+    "release": "0.6.5"
 }
\ No newline at end of file