From 4b0995f24ebdf0b76c00949ee2f5f92344191d63 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Feb 2026 17:45:54 +0100
Subject: [PATCH 1/5] Add missing filter_failed_collection_1.1.0.xml tool

Fixes #21389

The tool_conf.xml.sample references filter_failed_collection_1.1.0.xml
which did not exist. The filter_failed_collection.xml
(version 1.0.0) incorrectly had the "replacement" parameter which
should only be present in the 1.1.0 version. I chose to keep it
so that we don't cause issues with existing workflows and reruns.

This change:
- Creates filter_failed_collection_1.1.0.xml with the replacement
  parameter, following the pattern of other 1.1.0 tools like
  filter_empty_collection_1.1.0.xml
---
 .../tools/filter_failed_collection_1.1.0.xml  | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 lib/galaxy/tools/filter_failed_collection_1.1.0.xml

diff --git a/lib/galaxy/tools/filter_failed_collection_1.1.0.xml b/lib/galaxy/tools/filter_failed_collection_1.1.0.xml
new file mode 100644
index 00000000000..90ebb96f7a2
--- /dev/null
+++ b/lib/galaxy/tools/filter_failed_collection_1.1.0.xml
@@ -0,0 +1,66 @@
+<tool id="__FILTER_FAILED_DATASETS__"
+      name="Filter failed datasets"
+      version="1.1.0"
+      tool_type="filter_failed_datasets_collection">
+    <description></description>
+    <type class="FilterFailedDatasetsTool" module="galaxy.tools" />
+    <action module="galaxy.tools.actions.model_operations"
+            class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
+    <inputs>
+        <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
+        <param type="data" name="replacement" optional="true" label="Replace failed elements with this dataset" help="If provided, failed elements will be replaced with this dataset"/>
+    </inputs>
+    <outputs>
+        <collection name="output" format_source="input" type_source="input" label="${on_string} (filtered failed datasets)" >
+        </collection>
+    </outputs>
+    <tests>
+        <!-- Test framework has no way of creating a collection with
+             failed elements, so best we can do is verify identity on
+             an okay collection. API tests verify this tool works
+             though.
+        -->
+        <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="e1" value="simple_line.txt" />
+                </collection>
+            </param>
+            <output_collection name="output" type="list">
+                <element name="e1">
+                  <assert_contents>
+                      <has_text_matching expression="^This is a line of text.\n$" />
+                  </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+========
+Synopsis
+========
+
+Removes datasets in error (red) from a collection.
+
+===========
+Description
+===========
+
+This tool takes a dataset collection and filters out (removes) datasets in the failed (red) state. This is useful for continuing a multi-sample analysis when one or more of the samples fails at some point.
+
+.. image:: ${static_path}/images/tools/collection_ops/filter_error.svg
+  :width: 500
+  :alt: Filter failed datasets
+
+-----
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+      ]]></help>
+</tool>

From 0ab9d63bd77de875d135e7a60f458657823222e3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Feb 2026 18:00:37 +0100
Subject: [PATCH 2/5] Strip inline comments in conditional requirements

---
 lib/galaxy/dependencies/__init__.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 5afd18075b8..6b0f8599f36 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -3,6 +3,7 @@ Determine what optional dependencies are needed.
 """
 
 import os
+import re
 import sys
 from os.path import (
     dirname,
@@ -337,6 +338,12 @@ class ConditionalDependencies:
         return "huggingface" in self.file_sources
 
 
+def strip_comment(line):
+    # lifted from https://github.com/tox-dev/tox/commit/3c6b4f204e89852c4b7536b246a66d20be6d39ec
+    # xref https://github.com/pyupio/dparse/issues/34
+    return re.sub(r"\s+#.*", "", line).strip()
+
+
 def optional(config_file=None):
     if not config_file:
         config_file = find_config_file(["galaxy", "universe_wsgi"], include_samples=True)
@@ -347,5 +354,5 @@ def optional(config_file=None):
     conditional = ConditionalDependencies(config_file)
     for dependency in conditional.conditional_reqs:
         if conditional.check(dependency.name):
-            rval.append(dependency.line)
+            rval.append(strip_comment(dependency.line))
     return rval

From 72d245a875c99da947c4204528e6b552639f848c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 15 Jan 2026 08:10:46 -0500
Subject: [PATCH 3/5] Exclude node_modules at all depths in Docker builds

The pattern `node_modules` only matches at the root level in
.dockerignore (unlike .gitignore). Use `**/node_modules` to
exclude client/node_modules and avoid copying 22GB to the
build context.
---
 .dockerignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.dockerignore b/.dockerignore
index ce3827197e7..19a7dbeacb7 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,4 +1,4 @@
 .k8s_ci.Dockerfile
 .venv
 database
-node_modules
+**/node_modules

From af6230d66a92a820e2626eeb71acf5c68520a56d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Feb 2026 18:22:57 +0100
Subject: [PATCH 4/5] Add new filter from file version to sample tool conf

---
 lib/galaxy/config/sample/tool_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index 8b8c3c4a639..db08572fbcc 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -43,6 +43,7 @@
     <tool file="${model_tools_path}/merge_collection.xml" />
     <tool file="${model_tools_path}/relabel_from_file.xml" />
     <tool file="${model_tools_path}/filter_from_file.xml" />
+    <tool file="${model_tools_path}/filter_from_file_1.1.0.xml" />
     <tool file="${model_tools_path}/sort_collection_list.xml" />
     <tool file="${model_tools_path}/harmonize_two_collections_list.xml" />
     <tool file="${model_tools_path}/cross_product_flat.xml" />

From 6f7610aa2dc1ee80bb5862195c6f775951e209cf Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Feb 2026 20:14:52 +0100
Subject: [PATCH 5/5] Fix test formatting

---
 lib/galaxy_test/api/test_workflows.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 0a375f2631e..60d526d7b16 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -7972,8 +7972,7 @@ steps:
         # Regression test for https://github.com/galaxyproject/galaxy/issues/21602
         # When a workflow input with restrictOnConnections connects to multiple subworkflows,
         # the options should be the intersection of all connected subworkflow options.
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   Outer input parameter:
@@ -8013,8 +8012,7 @@ steps:
       in:
         select_ex:
           source: inner input parameter
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
         options = run_workflow["steps"][0]["inputs"][0]["options"]