From b280e5bca8d989f5270a375496bd9d8a87d78ff9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 17 Mar 2026 05:39:37 -0400
Subject: [PATCH] Fix PJAs corrupting skipped pick_value outputs

_apply_post_job_actions ran unconditionally, changing the datatype of
skipped HDAs (expression.json) away from expression.json. This broke
downstream skip detection. Guard with _is_null_or_skipped check.

Adds framework test: pick_value_skip_pja verifies skipped output
retains expression.json when ChangeDatatypeAction is configured.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/workflow/modules.py                |  4 ++-
 .../pick_value_skip_pja.gxwf-tests.yml        | 16 +++++++++++
 .../workflow/pick_value_skip_pja.gxwf.yml     | 28 +++++++++++++++++++
 3 files changed, 47 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy_test/workflow/pick_value_skip_pja.gxwf-tests.yml
 create mode 100644 lib/galaxy_test/workflow/pick_value_skip_pja.gxwf.yml

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 7979491f616..a4aac395402 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -2163,8 +2163,10 @@ class PickValueModule(WorkflowModule):
         """Apply post job actions directly to module output via ActionBox.
 
         Uses execute_on_mapped_over which operates on step_outputs dict
-        rather than requiring a Job object.
+        rather than requiring a Job object. Skipped outputs are left untouched.
         """
+        if self._is_null_or_skipped(output):
+            return
         step_outputs = {"output": output}
         step_inputs = {}
         for pja in step.post_job_actions:
diff --git a/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf-tests.yml b/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf-tests.yml
new file mode 100644
index 00000000000..333ff8ebbdf
--- /dev/null
+++ b/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf-tests.yml
@@ -0,0 +1,16 @@
+- doc: |
+    Test that PJAs are NOT applied to skipped outputs. When all inputs are
+    null, first_or_skip produces a skipped HDA (expression.json). The
+    ChangeDatatypeAction should not corrupt it.
+  job:
+    input_data:
+      type: File
+      value: 1.bed
+      file_type: bed
+    when:
+      type: raw
+      value: false
+  outputs:
+    picked:
+      class: File
+      ftype: expression.json
diff --git a/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf.yml b/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf.yml
new file mode 100644
index 00000000000..242217a9a43
--- /dev/null
+++ b/lib/galaxy_test/workflow/pick_value_skip_pja.gxwf.yml
@@ -0,0 +1,28 @@
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  when:
+    type: boolean
+outputs:
+  picked:
+    outputSource: pick/output
+steps:
+  branch:
+    tool_id: cat
+    in:
+      input1:
+        source: input_data
+      when:
+        source: when
+    when: $(inputs.when)
+  pick:
+    type: pick_value
+    in:
+      input_0:
+        source: branch/out_file1
+    state:
+      mode: first_or_skip
+    out:
+      output:
+        change_datatype: txt