diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index dd942966dd0..73874c5f601 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -20,12 +20,16 @@
                                 @click="submit('attribute', 'attributes')">
                                 <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
                             </b-button>
-                            <b-button @click="submit('attribute', 'autodetect')">
+                            <b-button v-if="!result['metadata_disable']" @click="submit('attribute', 'autodetect')">
                                 <font-awesome-icon icon="redo" class="mr-1" />{{ "Auto-detect" | l }}
                             </b-button>
                         </div>
                     </b-tab>
-                    <b-tab v-if="!result['conversion_disable'] || !result['datatype_disable']">
+                    <b-tab
+                        v-if="
+                            (!result['conversion_disable'] || !result['datatype_disable']) &&
+                            !result['metadata_disable']
+                        ">
                         <template v-slot:title>
                             <span v-if="!result['conversion_disable']">
                                 <font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}
diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.test.js b/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
index e0486579328..3fffa8e50ec 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
@@ -56,6 +56,11 @@ describe("History Navigation", () => {
             provide: { store },
         });
 
+        const createButton = wrapper.find("*[data-description='create new history']");
+        expect(createButton.attributes().disabled).toBeFalsy();
+        const switchButton = wrapper.find("*[data-description='switch to another history']");
+        expect(switchButton.attributes().disabled).toBeFalsy();
+
         const dropDown = wrapper.find("*[data-description='history options']");
         const optionElements = dropDown.findAll("b-dropdown-item-stub");
         const optionTexts = optionElements.wrappers.map((el) => el.text());
@@ -76,8 +81,12 @@ describe("History Navigation", () => {
             provide: { store },
         });
 
-        const dropDown = wrapper.find("*[data-description='history options']");
+        const createButton = wrapper.find("*[data-description='create new history']");
+        expect(createButton.attributes().disabled).toBeTruthy();
+        const switchButton = wrapper.find("*[data-description='switch to another history']");
+        expect(switchButton.attributes().disabled).toBeTruthy();
 
+        const dropDown = wrapper.find("*[data-description='history options']");
         const enabledOptionElements = dropDown.findAll("b-dropdown-item-stub:not([disabled])");
         const enabledOptionTexts = enabledOptionElements.wrappers.map((el) => el.text());
         expect(enabledOptionTexts).toStrictEqual(anonymousOptions);
diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 9d73f41cf6a..adc4d45a35e 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -12,7 +12,8 @@
                     data-description="create new history"
                     size="sm"
                     variant="link"
-                    title="Create new history"
+                    :disabled="currentUser.isAnonymous"
+                    :title="userTitle('Create new history')"
                     @click="$emit('createNewHistory')">
                     <Icon fixed-width icon="plus" />
                 </b-button>
@@ -23,7 +24,8 @@
                     data-description="switch to another history"
                     size="sm"
                     variant="link"
-                    title="Switch to history">
+                    :disabled="currentUser.isAnonymous"
+                    :title="userTitle('Switch to history')">
                     <Icon fixed-width icon="exchange-alt" />
                 </b-button>
 
diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index bc026247c84..121e911f63b 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -5,7 +5,7 @@ import SelectorModal from "./SelectorModal";
 
 const localVue = getLocalVue();
 
-const SELECTED_HISTORY_ID = "COOL_ID";
+const CURRENT_HISTORY_ID = "COOL_ID";
 const getFakeHistorySummaries = (num, selectedIndex = 0) => {
     const result = Array.from({ length: num }, (_, index) => ({
         id: `ID-${index}`,
@@ -13,11 +13,11 @@ const getFakeHistorySummaries = (num, selectedIndex = 0) => {
         tags: [],
         update_time: new Date().toISOString(),
     }));
-    result[selectedIndex].id = SELECTED_HISTORY_ID;
+    result[selectedIndex].id = CURRENT_HISTORY_ID;
     return result;
 };
 const PROPS_WITH_10_HISTORIES = {
-    currentHistoryId: SELECTED_HISTORY_ID,
+    currentHistoryId: CURRENT_HISTORY_ID,
     histories: getFakeHistorySummaries(10),
     perPage: 3,
     static: true, // Force the modal visible for testing
@@ -27,6 +27,8 @@ const PROPS_WITH_10_HISTORY_MULTIPLE_SELECT = {
     multiple: true,
 };
 
+const CURRENT_HISTORY_INDICATION_TEXT = "(Current)";
+
 describe("History SelectorModal.vue", () => {
     let wrapper;
 
@@ -38,12 +40,11 @@ describe("History SelectorModal.vue", () => {
         await flushPromises();
     }
 
-    it("should highlight the currently selected history", async () => {
+    it("should indicate the currently selected history", async () => {
         await mountWith(PROPS_WITH_10_HISTORIES);
 
-        const selectedRows = wrapper.findAll(".table-info");
-        expect(selectedRows.length).toBe(1);
-        expect(selectedRows.at(0).attributes("data-pk")).toBe(SELECTED_HISTORY_ID);
+        const currentHistoryRow = wrapper.find(`[data-pk="${CURRENT_HISTORY_ID}"]`);
+        expect(currentHistoryRow.html()).toContain(CURRENT_HISTORY_INDICATION_TEXT);
     });
 
     it("paginates the histories", async () => {
@@ -67,25 +68,29 @@ describe("History SelectorModal.vue", () => {
         expect(wrapper.emitted()["selectHistory"][0][0].id).toBe(targetHistoryId);
     });
 
-    it("select multiple histories", async () => {
-        await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
+    describe("Multi-selection Mode", () => {
+        it("should select multiple histories", async () => {
+            await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
 
-        expect(wrapper.emitted()["selectHistories"]).toBeUndefined();
+            expect(wrapper.emitted()["selectHistories"]).toBeUndefined();
 
-        const targetHistoryId1 = "ID-1";
-        const targetRow1 = wrapper.find(`[data-pk="${targetHistoryId1}"]`);
-        await targetRow1.trigger("click");
+            const targetHistoryId1 = "ID-1";
+            const targetRow1 = wrapper.find(`[data-pk="${targetHistoryId1}"]`);
+            await targetRow1.trigger("click");
 
-        const targetHistoryId2 = "ID-2";
-        const targetRow2 = wrapper.find(`[data-pk="${targetHistoryId2}"]`);
-        await targetRow2.trigger("click");
+            const targetHistoryId2 = "ID-2";
+            const targetRow2 = wrapper.find(`[data-pk="${targetHistoryId2}"]`);
+            await targetRow2.trigger("click");
 
-        expect(wrapper.vm.selectedHistories.length).toBe(2);
+            expect(wrapper.vm.selectedHistories.length).toBe(2);
 
-        const button = wrapper.find(".btn-primary");
+            const button = wrapper.find(".btn-primary");
 
-        await button.trigger("click");
+            await button.trigger("click");
 
-        expect(wrapper.emitted()["selectHistories"][0][0][0].id).toBe(targetHistoryId1);
+            expect(wrapper.emitted()["selectHistories"][0][0][0].id).toBe(targetHistoryId1);
+
+            console.debug(wrapper.html());
+        });
     });
 });
diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue
index 76dded0a196..5fdd0440798 100644
--- a/client/src/components/History/Modals/SelectorModal.vue
+++ b/client/src/components/History/Modals/SelectorModal.vue
@@ -11,7 +11,7 @@
             primary-key="id"
             :fields="fields"
             :filter="filter"
-            :items="formattedItems"
+            :items="histories"
             :per-page="perPage"
             :current-page="currentPage"
             :selectable="true"
@@ -22,6 +22,9 @@
             selected-variant="success"
             @row-selected="rowSelected"
             @filtered="onFiltered">
+            <template v-slot:cell(name)="row">
+                {{ row.item.name }} <i v-if="row.item.id === currentHistoryId"><b>(Current)</b></i>
+            </template>
             <template v-slot:cell(tags)="row">
                 <stateless-tags :value="row.item.tags" :disabled="true" />
             </template>
@@ -31,7 +34,9 @@
         </b-table>
         <template v-slot:modal-footer>
             <b-pagination v-model="currentPage" :total-rows="totalRows" :per-page="perPage" />
-            <b-button v-if="multiple" variant="primary" @click="addSelected">Add Selected</b-button>
+            <b-button v-if="multiple" :disabled="isEmptySelection" variant="primary" @click="addSelected">
+                Add Selected
+            </b-button>
         </template>
     </b-modal>
 </template>
@@ -69,13 +74,8 @@ export default {
         };
     },
     computed: {
-        formattedItems() {
-            return this.histories.map((item) => {
-                if (item.id === this.currentHistoryId) {
-                    item._rowVariant = "info";
-                }
-                return item;
-            });
+        isEmptySelection() {
+            return this.selectedHistories.length === 0;
         },
     },
     watch: {
diff --git a/client/src/components/LoadingSpan.vue b/client/src/components/LoadingSpan.vue
index 85e79a25c7e..c4c3b9d26b5 100644
--- a/client/src/components/LoadingSpan.vue
+++ b/client/src/components/LoadingSpan.vue
@@ -1,7 +1,7 @@
 <template>
     <span>
-        <span :class="spinnerClasses"></span>
-        <span class="loading-message">{{ message }}.<span class="blinking">..</span></span>
+        <span :class="spinnerClasses" title="loading"></span>
+        <span v-if="!spinnerOnly" class="loading-message">{{ message }}.<span class="blinking">..</span></span>
     </span>
 </template>
 <script>
@@ -16,6 +16,11 @@ export default {
             type: String,
             default: "Loading",
         },
+        spinnerOnly: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
     },
     computed: {
         spinnerClasses() {
diff --git a/client/src/components/Panels/Common/Tool.vue b/client/src/components/Panels/Common/Tool.vue
index be926ec04ed..7da41962ca2 100644
--- a/client/src/components/Panels/Common/Tool.vue
+++ b/client/src/components/Panels/Common/Tool.vue
@@ -59,9 +59,9 @@ export default {
     computed: {
         targetClass() {
             if (this.toolKey) {
-                return `tool-menu-item-${this.tool[this.toolKey]} title-link`;
+                return `tool-menu-item-${this.tool[this.toolKey]} title-link cursor-pointer`;
             } else {
-                return `title-link`;
+                return `title-link cursor-pointer`;
             }
         },
     },
diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue
index dd2a5303020..167659c2870 100644
--- a/client/src/components/Panels/Common/ToolSearch.vue
+++ b/client/src/components/Panels/Common/ToolSearch.vue
@@ -109,7 +109,7 @@ export default {
                     this.$emit("onResults", this.favoritesResults);
                 } else {
                     // keys with sorting order
-                    const keys = { exact: 2, name: 1, description: 0 };
+                    const keys = { exact: 3, name: 2, description: 1, combined: 0 };
                     this.$emit("onResults", searchToolsByKeys(this.toolsList, keys, q));
                 }
             } else {
diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
index 95e2dab6d48..bcb26c53f60 100644
--- a/client/src/components/Panels/ToolBoxWorkflow.vue
+++ b/client/src/components/Panels/ToolBoxWorkflow.vue
@@ -18,7 +18,7 @@
             <tool-search
                 :current-panel-view="currentPanelView"
                 placeholder="search tools"
-                :toolbox="toolbox"
+                :toolbox="workflowTools"
                 :query="query"
                 @onQuery="onQuery"
                 @onResults="onResults" />
@@ -74,7 +74,7 @@
 import _l from "utils/localization";
 import ToolSection from "./Common/ToolSection";
 import ToolSearch from "./Common/ToolSearch";
-import { filterToolSections } from "./utilities";
+import { filterToolSections, removeDisabledTools } from "./utilities";
 import PanelViewButton from "./Buttons/PanelViewButton";
 
 export default {
@@ -140,12 +140,13 @@ export default {
             };
         },
         sections() {
-            return filterToolSections(this.toolsLayout, this.results);
+            return filterToolSections(this.workflowTools, this.results);
         },
         toolsLayout() {
             return this.toolbox.map((section) => {
                 return {
                     ...section,
+                    disabled: !section.elems && !section.is_workflow_compatible,
                     elems:
                         section.elems &&
                         section.elems.map((el) => {
@@ -155,6 +156,9 @@ export default {
                 };
             });
         },
+        workflowTools() {
+            return removeDisabledTools(this.toolsLayout);
+        },
     },
     methods: {
         onQuery(query) {
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
index 8431e0828c1..eb86e05d0ed 100644
--- a/client/src/components/Panels/utilities.js
+++ b/client/src/components/Panels/utilities.js
@@ -89,7 +89,12 @@ export function searchToolsByKeys(tools, keys, query) {
     const returnedTools = [];
     for (const tool of tools) {
         for (const key of Object.keys(keys)) {
-            const actualValue = tool[key] ? tool[key].toLowerCase() : "";
+            let actualValue = "";
+            if (key === "combined") {
+                actualValue = tool.name.toLowerCase() + " " + tool.description.toLowerCase();
+            } else {
+                actualValue = tool[key] ? tool[key].toLowerCase() : "";
+            }
             const queryLowerCase = query.toLowerCase();
             if (actualValue.match(queryLowerCase)) {
                 // do we care for exact matches && is it an exact match ?
@@ -109,6 +114,22 @@ export function normalizeTools(tools) {
     return tools;
 }
 
+export function removeDisabledTools(tools) {
+    return tools.filter((section) => {
+        if (section.model_class === "ToolSectionLabel") {
+            return true;
+        } else if (!section.elems && section.disabled) {
+            return false;
+        } else if (section.elems) {
+            section.elems = section.elems.filter((el) => !el.disabled);
+            if (!section.elems.length) {
+                return false;
+            }
+        }
+        return true;
+    });
+}
+
 function flattenToolsSection(section) {
     const flattenTools = [];
     if (section.elems) {
diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js
index eb6fdadad6f..05697266a11 100644
--- a/client/src/components/Panels/utilities.test.js
+++ b/client/src/components/Panels/utilities.test.js
@@ -17,7 +17,7 @@ describe("test helpers in tool searching utilities", () => {
     });
 
     it("test tool search helper that searches for tools given keys", async () => {
-        const q = "collection";
+        let q = "collection";
         let expectedResults = [
             "__FILTER_FAILED_DATASETS__",
             "__FILTER_EMPTY_DATASETS__",
@@ -37,6 +37,12 @@ describe("test helpers in tool searching utilities", () => {
         keys = { description: 0, name: 1 };
         results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
+
+        q = "filter empty datasets";
+        expectedResults = ["__FILTER_EMPTY_DATASETS__"];
+        keys = { description: 1, name: 2, combined: 0 };
+        results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
+        expect(results).toEqual(expectedResults);
     });
 
     it("test tool filtering helpers on toolsList given list of ids", async () => {
diff --git a/client/src/components/Workflow/Editor/Forms/FormTool.test.js b/client/src/components/Workflow/Editor/Forms/FormTool.test.js
index 2db5af07c0e..01bdcfb973c 100644
--- a/client/src/components/Workflow/Editor/Forms/FormTool.test.js
+++ b/client/src/components/Workflow/Editor/Forms/FormTool.test.js
@@ -11,9 +11,7 @@ import { createTestingPinia } from "@pinia/testing";
 const localVue = getLocalVue();
 
 describe("FormTool", () => {
-    let wrapper;
-
-    beforeEach(() => {
+    function mountTarget() {
         const store = new Vuex.Store({
             modules: {
                 user: mockModule(userStore),
@@ -21,7 +19,7 @@ describe("FormTool", () => {
             },
         });
 
-        wrapper = mount(FormTool, {
+        return mount(FormTool, {
             propsData: {
                 id: "input",
                 datatypes: [],
@@ -32,7 +30,7 @@ describe("FormTool", () => {
                         name: "tool_name",
                         version: "1.0",
                         description: "description",
-                        inputs: [],
+                        inputs: [{ name: "input", label: "input", type: "text", value: "value" }],
                         help: "help_text",
                         versions: ["1.0", "2.0", "3.0"],
                         citations: false,
@@ -46,15 +44,16 @@ describe("FormTool", () => {
             stubs: {
                 CurrentUser: MockCurrentUser({ id: "fakeuser" }),
                 ConfigProvider: MockConfigProvider({ id: "fakeconfig" }),
-                FormElement: { template: "<div>form-element</div>" },
                 ToolFooter: { template: "<div>tool-footer</div>" },
             },
             pinia: createTestingPinia(),
             provide: { store },
         });
-    });
+    }
 
     it("changes between different versions", async () => {
+        const wrapper = mountTarget();
+
         const dropdowns = wrapper.findAll(".tool-versions .dropdown-item");
         let version = dropdowns.at(1);
         expect(version.text()).toBe("Switch to 2.0");
diff --git a/client/src/components/Workflow/Editor/Forms/FormTool.vue b/client/src/components/Workflow/Editor/Forms/FormTool.vue
index 609447c15a9..2d8e70e2972 100644
--- a/client/src/components/Workflow/Editor/Forms/FormTool.vue
+++ b/client/src/components/Workflow/Editor/Forms/FormTool.vue
@@ -163,9 +163,16 @@ export default {
         onLabel(newLabel) {
             this.$emit("onLabel", this.stepId, newLabel);
         },
+        /**
+         * Change event is triggered on component creation and input changes.
+         * @param { Object } values contains flat key-value pairs `prefixed-name=value`
+         */
         onChange(values) {
+            const initialRequest = Object.keys(this.mainValues).length === 0;
             this.mainValues = values;
-            this.postChanges();
+            if (!initialRequest) {
+                this.postChanges();
+            }
         },
         onChangePostJobActions(postJobActions) {
             this.$emit("onChangePostJobActions", this.stepId, postJobActions);
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 92ee4af0680..34362b5f2ff 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -108,6 +108,7 @@
                             <div>
                                 <FormTool
                                     v-if="hasActiveNodeTool"
+                                    :key="activeStep.id"
                                     :step="activeStep"
                                     :datatypes="datatypes"
                                     @onChangePostJobActions="onChangePostJobActions"
@@ -253,6 +254,10 @@ export default {
         const hasChanges = ref(false);
         const hasInvalidConnections = computed(() => Object.keys(connectionsStore.invalidConnections).length > 0);
 
+        stepStore.$subscribe((mutation, state) => {
+            hasChanges.value = true;
+        });
+
         function resetStores() {
             connectionsStore.$reset();
             stepStore.$reset();
@@ -341,9 +346,6 @@ export default {
                 this.hasChanges = true;
             }
         },
-        steps(newSteps, oldSteps) {
-            this.hasChanges = true;
-        },
         hasChanges() {
             this.$emit("update:confirmation", this.hasChanges);
         },
@@ -356,7 +358,6 @@ export default {
     methods: {
         onUpdateStep(step) {
             this.stepStore.updateStep(step);
-            this.hasChanges = true;
         },
         onUpdateStepPosition(stepId, position) {
             const step = { ...this.steps[stepId], position };
@@ -408,6 +409,7 @@ export default {
             hide_modal(); // hide other modals created in utilities also...
         },
         async onRefactor(response) {
+            this.resetStores();
             await fromSimple(response.workflow);
             this._loadEditorData(response.workflow);
         },
diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index 3a475c5ceb2..0d7abe9abd6 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -11,8 +11,8 @@
         @move="onMoveTo"
         @pan-by="onPanBy">
         <div class="node-header unselectable clearfix" @click="makeActive" @keyup.enter="makeActive">
-            <loading-span v-if="isLoading" message="Loading details" />
             <b-button-group class="float-right">
+                <loading-span v-if="isLoading" spinner-only />
                 <b-button
                     v-if="canClone"
                     v-b-tooltip.hover
diff --git a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
index db69f9e509e..50916494f52 100644
--- a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
+++ b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
@@ -3,7 +3,7 @@ import { ref } from "vue";
 
 export function useUniqueLabelError(
     workflowStateStore: ReturnType<typeof useWorkflowStepStore>,
-    label: string | undefined
+    label: string | null | undefined
 ) {
     const error = ref("");
     if (label && workflowStateStore.workflowOutputs[label]) {
diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index f71de5dabbf..154477afb7f 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -1,6 +1,6 @@
 import { setActivePinia, createPinia } from "pinia";
 
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import { useWorkflowStepStore, type TerminalSource } from "@/stores/workflowStepStore";
 import {
     terminalFactory,
     InputCollectionTerminal,
@@ -15,7 +15,11 @@ import {
 import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import type { DataOutput, Steps } from "@/stores/workflowStepStore";
-import { NULL_COLLECTION_TYPE_DESCRIPTION } from "./collectionTypeDescription";
+import {
+    ANY_COLLECTION_TYPE_DESCRIPTION,
+    CollectionTypeDescription,
+    NULL_COLLECTION_TYPE_DESCRIPTION,
+} from "./collectionTypeDescription";
 import { simpleSteps, advancedSteps } from "../test_fixtures";
 
 function setupAdvanced() {
@@ -35,6 +39,17 @@ function setupAdvanced() {
     return terminals;
 }
 
+function rebuildTerminal<T extends ReturnType<typeof terminalFactory>>(terminal: T): T {
+    let terminalSource: TerminalSource;
+    const step = terminal.stepStore.getStep(terminal.stepId);
+    if (terminal.terminalType === "input") {
+        terminalSource = step.inputs.find((input) => input.name == terminal.name)!;
+    } else {
+        terminalSource = step.outputs.find((output) => output.name == terminal.name)!;
+    }
+    return terminalFactory(terminal.stepId, terminalSource, testDatatypesMapper) as T;
+}
+
 describe("terminalFactory", () => {
     let terminals: { [index: string]: { [index: string]: ReturnType<typeof terminalFactory> } } = {};
     beforeEach(() => {
@@ -64,6 +79,8 @@ describe("terminalFactory", () => {
         expect(terminals["any collection"]["output"]).toBeInstanceOf(OutputCollectionTerminal);
         expect(terminals["multi data"]["advanced|advanced_threshold"]).toBeInstanceOf(InputParameterTerminal);
         expect(terminals["list collection input"]["input1"]).toBeInstanceOf(InputCollectionTerminal);
+        expect(terminals["filter_failed"]["input"]).toBeInstanceOf(InputCollectionTerminal);
+        expect(terminals["filter_failed"]["output"]).toBeInstanceOf(OutputCollectionTerminal);
     });
     it("throws error on invalid terminalSource", () => {
         const invalidFactory = () => terminalFactory(1, {} as any, testDatatypesMapper);
@@ -257,7 +274,7 @@ describe("canAccept", () => {
             "Can't map over this input with output collection type - this step has outputs defined constraining the mapping of this tool. Disconnect outputs and retry."
         );
     });
-    it("rejects attaching non-collection outputs to mapper over inputs", () => {
+    it("rejects attaching non-collection outputs to mapped-over inputs", () => {
         const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
         const simpleDataOut = terminals["data input"]["output"] as OutputTerminal;
         const dataIn = terminals["simple data"]["input"] as InputTerminal;
@@ -281,11 +298,7 @@ describe("canAccept", () => {
         dataInTwo.disconnect(dataOut);
         // terminal isn't a reactive class in any way (worth a thought doing, but difficult!), the following happens when a new terminal is built
         // in useTerminal.ts
-        const rebuiltDataIn = terminalFactory(
-            dataIn.stepId,
-            advancedSteps[dataIn.stepId].inputs[0],
-            testDatatypesMapper
-        );
+        const rebuiltDataIn = rebuildTerminal(dataIn);
         expect(rebuiltDataIn.localMapOver.isCollection).toBe(false);
         expect(rebuiltDataIn.canAccept(simpleDataOut).canAccept).toBe(true);
     });
@@ -389,7 +402,9 @@ describe("canAccept", () => {
         const collectionOut = terminals["list:list input"]["output"] as OutputCollectionTerminal;
         const collectionIn = terminals["list collection input"]["input1"] as InputCollectionTerminal;
         expect(collectionIn.canAccept(collectionOut).canAccept).toBe(true);
+        expect(collectionIn.isMappedOver()).toBe(false);
         collectionIn.connect(collectionOut);
+        expect(collectionIn.isMappedOver()).toBe(true);
         expect(collectionIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         const intermediateOut = terminals["list collection input"]["out_file1"] as OutputCollectionTerminal;
         const otherListIn = terminals["list collection input 2"]["input1"] as InputCollectionTerminal;
@@ -459,6 +474,20 @@ describe("canAccept", () => {
             "Effective output data type(s) [tabular] do not appear to match input type(s) [ab1]."
         );
     });
+    it("resolves collection type source", () => {
+        const filterFailedInput = terminals["filter_failed"]["input"] as InputCollectionTerminal;
+        const filterFailedOutput = terminals["filter_failed"]["output"] as OutputCollectionTerminal;
+        expect(filterFailedOutput.collectionType).toBe(ANY_COLLECTION_TYPE_DESCRIPTION);
+        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+        filterFailedInput.connect(collectionOut);
+        expect(rebuildTerminal(filterFailedOutput).collectionType).toStrictEqual(new CollectionTypeDescription("list"));
+        filterFailedInput.disconnect(collectionOut);
+        const listPairedOutput = terminals["list:paired input"]["output"] as OutputCollectionTerminal;
+        filterFailedInput.connect(listPairedOutput);
+        expect(rebuildTerminal(filterFailedOutput).collectionType).toStrictEqual(
+            new CollectionTypeDescription("list:paired")
+        );
+    });
 });
 
 describe("Input terminal", () => {
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 1e354149ffa..f6f4cc149cb 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -97,6 +97,7 @@ class Terminal extends EventEmitter {
         this.resetMappingIfNeeded(connection);
     }
     setMapOver(val: CollectionTypeDescriptor) {
+        // we use this method to determine the map over status based on all terminals connected to this step
         let outputVal = val;
         if (this.multiple) {
             // emulate list input
@@ -112,7 +113,11 @@ class Terminal extends EventEmitter {
             this.stepStore.changeStepInputMapOver(this.stepId, this.name, effectiveMapOver);
             this.localMapOver = effectiveMapOver;
         }
-        if (!this.mapOver.equal(effectiveMapOver)) {
+        if (
+            !this.mapOver.equal(effectiveMapOver) &&
+            (effectiveMapOver.isCollection ||
+                !Object.values(this.stepStore.stepInputMapOver[this.stepId]).find((mapOver) => mapOver.isCollection))
+        ) {
             this.stepStore.changeStepMapOver(this.stepId, effectiveMapOver);
         }
     }
@@ -242,6 +247,11 @@ class BaseInputTerminal extends Terminal {
         }
         return null;
     }
+
+    isMappedOver(): boolean {
+        return Boolean(this.localMapOver.isCollection);
+    }
+
     connected() {
         return Boolean(this._getFirstOutputTerminal());
     }
@@ -400,10 +410,6 @@ export class InputTerminal extends BaseInputTerminal {
         this.getStepMapOver();
     }
 
-    isMappedOver(): boolean {
-        return Boolean(this.localMapOver.isCollection);
-    }
-
     attachable(other: BaseOutputTerminal) {
         const otherCollectionType = this._otherCollectionType(other);
         const mapOver = this.mapOver;
@@ -490,10 +496,10 @@ export class InputParameterTerminal extends BaseInputTerminal {
         const effectiveThisType = this.effectiveType(this.type);
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
-        const canAccept = effectiveThisType === effectiveOtherType
+        const canAccept = effectiveThisType === effectiveOtherType;
         return new ConnectionAcceptable(
             canAccept,
-            canAccept ? null: `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
+            canAccept ? null : `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
         );
     }
 }
@@ -672,19 +678,56 @@ interface OutputCollectionTerminalArgs extends BaseOutputTerminalArgs {
 }
 
 export class OutputCollectionTerminal extends BaseOutputTerminal {
+    collectionTypeSource: string | null;
+
     constructor(attr: OutputCollectionTerminalArgs) {
         super(attr);
+        this.collectionTypeSource = null;
         if (attr.collection_type) {
             this.collectionType = new CollectionTypeDescription(attr.collection_type);
         } else {
-            const collectionTypeSource = attr.collection_type_source;
-            if (!collectionTypeSource) {
+            this.collectionTypeSource = attr.collection_type_source;
+            if (!this.collectionTypeSource) {
                 console.log("Warning: No collection type or collection type source defined.");
             }
-            this.collectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
+            this.collectionType = this.getCollectionTypeFromInput() || ANY_COLLECTION_TYPE_DESCRIPTION;
         }
         this.isCollection = true;
     }
+
+    getCollectionTypeFromInput() {
+        const connection = this.connectionStore.connections.find(
+            (connection) =>
+                connection.input.name === this.collectionTypeSource && connection.input.stepId === this.stepId
+        );
+        if (connection) {
+            const outputStep = this.stepStore.getStep(connection.output.stepId);
+            const inputStep = this.stepStore.getStep(this.stepId);
+            if (outputStep) {
+                const stepOutput = outputStep.outputs.find((output) => output.name == connection.output.name);
+                const stepInput = inputStep.inputs.find((input) => input.name === this.collectionTypeSource);
+                if (stepInput && stepOutput) {
+                    const outputTerminal = terminalFactory(connection.output.stepId, stepOutput, this.datatypesMapper);
+                    const inputTerminal = terminalFactory(connection.output.stepId, stepInput, this.datatypesMapper);
+                    // otherCollectionType is the mapped over output collection as it would appear at the input terminal
+                    const otherCollectionType = inputTerminal._otherCollectionType(outputTerminal);
+                    // we need to find which of the possible input collection types is connected
+                    if ("collectionTypes" in inputTerminal) {
+                        // collection_type_source must point at input collection terminal
+                        const connectedCollectionType = inputTerminal.collectionTypes.find(
+                            (collectionType) =>
+                                otherCollectionType.canMatch(collectionType) ||
+                                otherCollectionType.canMapOver(collectionType)
+                        );
+                        if (connectedCollectionType) {
+                            return connectedCollectionType;
+                        }
+                    }
+                }
+            }
+        }
+        return ANY_COLLECTION_TYPE_DESCRIPTION;
+    }
 }
 
 interface OutputParameterTerminalArgs extends Omit<BaseOutputTerminalArgs, "datatypes"> {
diff --git a/client/src/components/Workflow/Editor/test-data/parameter_steps.json b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
index fb9a9ed0f02..d3cff2cf8d9 100644
--- a/client/src/components/Workflow/Editor/test-data/parameter_steps.json
+++ b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
@@ -812,5 +812,99 @@
       "left": 70.45245361328125,
       "top": 316.3525695800781
     }
+  },
+  "17": {
+    "id": 17,
+    "type": "tool",
+    "label": "filter_failed",
+    "content_id": "__FILTER_FAILED_DATASETS__",
+    "name": "Filter failed datasets",
+    "tool_state": {
+      "input": "{\"__class__\": \"RuntimeValue\"}",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [
+      {
+        "name": "input",
+        "label": "Input Collection",
+        "multiple": false,
+        "input_type": "dataset_collection",
+        "collection_types": [
+          "list",
+          "list:paired"
+        ],
+        "optional": false,
+        "extensions": [
+          "data"
+        ]
+      }
+    ],
+    "outputs": [
+      {
+        "name": "output",
+        "extensions": [
+          "input"
+        ],
+        "type": "collection",
+        "optional": false,
+        "collection": true,
+        "collection_type": null,
+        "collection_type_source": "input",
+        "label": "input dataset(s) (filtered failed datasets)"
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "uuid": "f5de18b9-b08e-4160-b71b-54768a4e5208",
+    "when": null,
+    "workflow_outputs": [
+      {
+        "output_name": "output",
+        "uuid": "3774e554-b7d1-41ba-9acd-ee82ba9fbf54",
+        "label": null
+      }
+    ],
+    "input_connections": {},
+    "position": {
+      "left": 0,
+      "top": 0
+    }
+  },
+  "18": {
+    "id": 18,
+    "type": "data_collection_input",
+    "label": "list:paired input",
+    "content_id": null,
+    "name": "Input dataset collection",
+    "tool_state": {
+      "collection_type": "\"list:paired\"",
+      "optional": "\"false\"",
+      "tag": "\"\"",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [],
+    "outputs": [
+      {
+        "name": "output",
+        "extensions": [
+          "input"
+        ],
+        "collection": true,
+        "collection_type": "list:paired",
+        "optional": false
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "workflow_outputs": [],
+    "input_connections": {},
+    "position": {
+      "left": 12.8729248046875,
+      "top": 501.7839660644531
+    }
   }
 }
diff --git a/client/src/stores/workflowConnectionStore.ts b/client/src/stores/workflowConnectionStore.ts
index 7748a417e77..cacd54e14f6 100644
--- a/client/src/stores/workflowConnectionStore.ts
+++ b/client/src/stores/workflowConnectionStore.ts
@@ -34,6 +34,7 @@ export interface BaseTerminal {
 
 export interface InputTerminal extends BaseTerminal {
     connectorType: "input";
+    input_subworkflow_step_id?: number;
 }
 
 export interface OutputTerminal extends BaseTerminal {
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 655f6735c7d..20057d984f1 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -63,6 +63,7 @@ interface BaseStepInput {
     extensions: string[];
     optional: boolean;
     input_type: string;
+    input_subworkflow_step_id?: number;
 }
 
 export interface DataStepInput extends BaseStepInput {
@@ -85,8 +86,8 @@ export type TerminalSource = InputTerminalSource | OutputTerminalSource;
 
 interface WorkflowOutput {
     output_name: string;
-    label?: string;
-    uuid?: string;
+    label?: string | null;
+    uuid?: string | null;
 }
 
 export interface NewStep {
@@ -97,7 +98,7 @@ export interface NewStep {
     errors?: string[] | null;
     input_connections: StepInputConnection;
     inputs: Array<InputTerminalSource>;
-    label?: string;
+    label?: string | null;
     name: string;
     outputs: Array<OutputTerminalSource>;
     position?: StepPosition;
@@ -106,7 +107,7 @@ export interface NewStep {
     tooltip?: string;
     type: "tool" | "data_input" | "data_collection_input" | "subworkflow" | "parameter_input" | "pause";
     uuid?: string;
-    when?: string;
+    when?: string | null;
     workflow_outputs?: WorkflowOutput[];
 }
 
@@ -125,6 +126,7 @@ export interface StepInputConnection {
 export interface ConnectionOutputLink {
     output_name: string;
     id: number;
+    input_subworkflow_step_id?: number;
 }
 
 interface WorkflowOutputs {
@@ -231,11 +233,19 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
         },
         addConnection(connection: Connection) {
             const inputStep = this.getStep(connection.input.stepId);
+            const input = inputStep.inputs.find((input) => input.name === connection.input.name);
+            const connectionLink: ConnectionOutputLink = {
+                output_name: connection.output.name,
+                id: connection.output.stepId,
+            };
+            if (input && "input_subworkflow_step_id" in input && input.input_subworkflow_step_id !== undefined) {
+                connectionLink["input_subworkflow_step_id"] = input.input_subworkflow_step_id;
+            }
             const updatedStep = {
                 ...inputStep,
                 input_connections: {
                     ...inputStep.input_connections,
-                    [connection.input.name]: { output_name: connection.output.name, id: connection.output.stepId },
+                    [connection.input.name]: connectionLink,
                 },
             };
             this.updateStep(updatedStep);
@@ -258,7 +268,7 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
 export function stepToConnections(step: Step): Connection[] {
     const connections: Connection[] = [];
     if (step.input_connections) {
-        Object.entries(step?.input_connections).forEach(([input_name, outputArray]) => {
+        Object.entries(step?.input_connections).forEach(([inputName, outputArray]) => {
             if (outputArray === undefined) {
                 return;
             }
@@ -269,7 +279,7 @@ export function stepToConnections(step: Step): Connection[] {
                 const connection = new Connection(
                     {
                         stepId: step.id,
-                        name: input_name,
+                        name: inputName,
                         connectorType: "input",
                     },
                     {
@@ -278,6 +288,10 @@ export function stepToConnections(step: Step): Connection[] {
                         connectorType: "output",
                     }
                 );
+                const connectionInput = step.inputs.find((input) => input.name == inputName);
+                if (connectionInput && "input_subworkflow_step_id" in connectionInput) {
+                    connection.input.input_subworkflow_step_id = connectionInput.input_subworkflow_step_id;
+                }
                 connections.push(connection);
             });
         });
diff --git a/config/plugins/tours/core.windows.yaml b/config/plugins/tours/core.windows.yaml
index 226150dadf6..d2318ce3c5d 100644
--- a/config/plugins/tours/core.windows.yaml
+++ b/config/plugins/tours/core.windows.yaml
@@ -6,15 +6,14 @@ tags:
   - "UI"
   - "visualization"
 
+requirements:
+  - new_history
+
 steps:
     - content: "This short tour will walk you through <b>Galaxy's Window Manager</b> feature"
 
-    - element: "#current-history-panel .create-hist-btn"
-      intro: "Before using the Window Manager, we will create a new history for this tour."
-      postclick: true
-
     - element: "#tool-panel-upload-button"
-      intro: "Now, we will upload some tabular data into our new history."
+      intro: "First, we will upload some tabular data into our new history."
       postclick: true
 
     - element: "#btn-new"
@@ -78,7 +77,7 @@ steps:
 
     - element: "#right"
       intro: "This is your history. It contains our two tables being uploaded."
-    
+
     - component: history_panel.item(hid=1,state=ok).display_button
       intro: "Clicking the eye-icon usually displays a dataset in the center panel."
       postclick: true
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 5e963fbde85..8375e61e572 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7163,8 +7163,20 @@ class WorkflowStep(Base, RepresentById):
         conn.output_name = output_name
         add_object_to_object_session(conn, output_step)
         conn.output_step = output_step
-        if input_subworkflow_step_index is not None:
-            input_subworkflow_step = self.subworkflow.step_by_index(input_subworkflow_step_index)
+        if self.subworkflow:
+            if input_subworkflow_step_index is not None:
+                input_subworkflow_step = self.subworkflow.step_by_index(input_subworkflow_step_index)
+            else:
+                input_subworkflow_steps = [step for step in self.subworkflow.input_steps if step.label == input_name]
+                if not input_subworkflow_steps:
+                    inferred_order_index = input_name.split(":", 1)[0]
+                    if inferred_order_index.isdigit():
+                        input_subworkflow_steps = [self.subworkflow.step_by_index(int(inferred_order_index))]
+                if len(input_subworkflow_steps) != 1:
+                    raise galaxy.exceptions.MessageException(
+                        f"Invalid subworkflow connection at step index {self.order_index + 1}"
+                    )
+                input_subworkflow_step = input_subworkflow_steps[0]
             conn.input_subworkflow_step = input_subworkflow_step
         return conn
 
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index 467c6070f66..5f0bd18563c 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -4,12 +4,10 @@ adapt cwltool to Galaxy features and abstract the library away from the rest
 of the framework.
 """
 
-import base64
 import copy
 import json
 import logging
 import os
-import pickle
 from abc import (
     ABCMeta,
     abstractmethod,
@@ -31,7 +29,6 @@ from galaxy.exceptions import MessageException
 from galaxy.util import (
     listify,
     safe_makedirs,
-    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from .cwltool_deps import (
@@ -86,8 +83,6 @@ SUPPORTED_TOOL_REQUIREMENTS = [
 
 SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + []
 
-PERSISTED_REPRESENTATION = "cwl_tool_object"
-
 ToolStateType = Dict[str, Union[None, str, bool, Dict[str, str]]]
 
 
@@ -173,29 +168,29 @@ class ToolProxy(metaclass=ABCMeta):
     def to_persistent_representation(self):
         """Return a JSON representation of this tool. Not for serialization
         over the wire, but serialization in a database."""
-        # TODO: Replace this with some more readable serialization,
-        # I really don't like using pickle here.
-        if PERSISTED_REPRESENTATION == "cwl_tool_object":
-            persisted_obj = remove_pickle_problems(self._tool)
-        else:
-            persisted_obj = self._raw_process_reference
+        persisted_obj = self._tool.tool
+        persisted_obj["requirements"] = self.requirements
+        if not persisted_obj.get("cwlVersion"):
+            # This happens for any inline process, but getting it from metadata is correct for inline processes at least
+            persisted_obj["cwlVersion"] = self._tool.metadata["cwlVersion"]
         return {
             "class": self._class,
-            "pickle": unicodify(base64.b64encode(pickle.dumps(persisted_obj, pickle.HIGHEST_PROTOCOL))),
+            # Should maybe be yaml instead
+            "raw_process_reference": persisted_obj,
             "uuid": self.uuid,
         }
 
     @staticmethod
-    def from_persistent_representation(as_object) -> "ToolProxy":
+    def from_persistent_representation(as_object, strict_cwl_validation=True, tool_directory=None) -> "ToolProxy":
         """Recover an object serialized with to_persistent_representation."""
         if "class" not in as_object:
             raise Exception("Failed to deserialize tool proxy from JSON object - no class found.")
-        if "pickle" not in as_object:
-            raise Exception("Failed to deserialize tool proxy from JSON object - no pickle representation found.")
-        if "uuid" not in as_object:
-            raise Exception("Failed to deserialize tool proxy from JSON object - no uuid found.")
-        to_unpickle = base64.b64decode(as_object["pickle"])
-        loaded_object = pickle.loads(to_unpickle)
+        loaded_object = tool_proxy(
+            tool_object=as_object["raw_process_reference"],
+            strict_cwl_validation=strict_cwl_validation,
+            tool_directory=tool_directory,
+            uuid=as_object.get("uuid"),
+        )
         return loaded_object
 
     @property
@@ -743,14 +738,8 @@ def tool_proxy_from_persistent_representation(
 ) -> ToolProxy:
     """Load a ToolProxy from a previously persisted representation."""
     ensure_cwltool_available()
-    if PERSISTED_REPRESENTATION == "cwl_tool_object":
-        kwds = {"cwl_tool_object": ToolProxy.from_persistent_representation(persisted_tool)}
-    else:
-        raw_process_reference = persisted_tool  # ???
-        kwds = {"raw_process_reference": ToolProxy.from_persistent_representation(raw_process_reference)}
-    uuid = persisted_tool["uuid"]
-    return _to_cwl_tool_object(
-        uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds
+    return ToolProxy.from_persistent_representation(
+        persisted_tool, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory
     )
 
 
@@ -765,15 +754,10 @@ def load_job_proxy(job_directory, strict_cwl_validation=True) -> JobProxy:
     job_objects = json.load(open(job_objects_path))
     job_inputs = job_objects["job_inputs"]
     output_dict = job_objects["output_dict"]
-    # Any reason to retain older tool_path variant of this? Probably not?
-    if "tool_path" in job_objects:
-        tool_path = job_objects["tool_path"]
-        cwl_tool = tool_proxy(tool_path, strict_cwl_validation=strict_cwl_validation)
-    else:
-        persisted_tool = job_objects["tool_representation"]
-        cwl_tool = tool_proxy_from_persistent_representation(
-            persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation
-        )
+    persisted_tool = job_objects["tool_representation"]
+    cwl_tool = tool_proxy_from_persistent_representation(
+        persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation
+    )
     return cwl_tool.job_proxy(job_inputs, output_dict, job_directory=job_directory)
 
 
@@ -1107,17 +1091,6 @@ class SubworkflowStepProxy(BaseStepProxy):
         return self._subworkflow_proxy
 
 
-def remove_pickle_problems(obj):
-    """doc_loader does not pickle correctly"""
-    if hasattr(obj, "doc_loader"):
-        obj.doc_loader = None
-    if hasattr(obj, "embedded_tool"):
-        obj.embedded_tool = remove_pickle_problems(obj.embedded_tool)
-    if hasattr(obj, "steps"):
-        obj.steps = [remove_pickle_problems(s) for s in obj.steps]
-    return obj
-
-
 def _outer_field_to_input_instance(field):
     field_type = field_to_field_type(field)  # Must be a list if in here?
     if not isinstance(field_type, list):
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 0473f7d2a1f..fe1578907b9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -291,6 +291,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if data.missing_meta():
                 message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
                 status = "warning"
+            metadata_disable = data.state not in [
+                trans.model.Dataset.states.OK,
+                trans.model.Dataset.states.FAILED_METADATA,
+            ]
             # datatype conversion
             conversion_options = [
                 (f"{convert_id} (using '{convert_name}')", convert_id)
@@ -369,6 +373,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 "message": message,
                 "status": status,
                 "dataset_id": dataset_id,
+                "metadata_disable": metadata_disable,
                 "attribute_inputs": attribute_inputs,
                 "conversion_inputs": conversion_inputs,
                 "conversion_disable": conversion_disable,
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 4f5e1553325..92bbd17a2aa 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -2051,6 +2051,8 @@ steps:
       inputs:
         some_file:
           type: data
+        should_run:
+          type: boolean
       steps:
         a_tool_step:
           tool_id: cat1
@@ -2154,6 +2156,7 @@ steps:
       class: GalaxyWorkflow
       inputs:
         boolean_input_file: data
+        should_run: boolean
       steps:
         consume_expression_parameter:
           tool_id: cat1
diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py
index 0178e935dae..0f164c087b0 100644
--- a/lib/galaxy_test/base/workflow_fixtures.py
+++ b/lib/galaxy_test/base/workflow_fixtures.py
@@ -1012,6 +1012,7 @@ steps:
       class: GalaxyWorkflow
       inputs:
         boolean_input_file: data
+        should_run: boolean
       steps:
         create_more_inputs:
           tool_id: collection_creates_dynamic_nested
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 9be68ab210c..eb40f60ff96 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -697,7 +697,10 @@ steps:
         workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
         parent_workflow_id = workflow_populator.upload_yaml_workflow(
             """class: GalaxyWorkflow
-inputs: []
+inputs:
+  input_collection:
+    type: collection
+    collection_type: "list"
 steps:
   - tool_id: multiple_versions
     tool_version: 0.1
@@ -716,10 +719,16 @@ steps:
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(parent_workflow_id)
-        subworkflow_step = workflow["steps"]["1"]
+        subworkflow_step = workflow["steps"]["2"]
         assert subworkflow_step["name"] == child_workflow_name
         assert subworkflow_step["type"] == "subworkflow"
         assert subworkflow_step["subworkflow"]["a_galaxy_workflow"] == "true"
+        self.workflow_editor_connect("input_collection#output", f"{child_workflow_name}#input1")
+        self.assert_connected("input_collection#output", f"{child_workflow_name}#input1")
+        self.assert_workflow_has_changes_and_save()
+        workflow = self.workflow_populator.download_workflow(parent_workflow_id)
+        subworkflow_step = workflow["steps"]["2"]
+        assert subworkflow_step["input_connections"]["input1"]["input_subworkflow_step_id"] == 0
 
     @selenium_test
     def test_editor_insert_steps(self):