Add test for filename conflict resolution

Added a test that verifies that the fix in DataBiosphere#4101 avoids incorrect filename conflict resolution.

src/toil/test/cwl/cwlTest.py

@@ -996,6 +996,25 @@ def test_log_dir_echo_stderr(self) -> None:
         output = open(result).read()
         assert output == "hello\n"
 
+    def test_filename_conflict_resolution(self):
+        toil = "toil-cwl-runner"
+        options = [
+            f"--outdir={self.out_dir}",
+            "--clean=always",
+        ]
+        cwl = os.path.join(
+            os.path.dirname(__file__), "test_filename_conflict_resolution.cwl"
+        )
+        input = os.path.join(os.path.dirname(__file__), "test_filename_conflict_resolution.ms")
+        output = input + '.sector_*'
+        cwl_inputs = [
+            "--msin", input
+        ]
+        cmd = [toil] + options + [cwl] + cwl_inputs
+        p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        stdout, stderr = p.communicate()
+        assert b"Finished toil run successfully" in stderr
+        assert p.returncode == 0
 
 @needs_cwl
 class CWLSmallTests(ToilTest):

src/toil/test/cwl/test_filename_conflict_resolution.cwl

@@ -0,0 +1,31 @@
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - python
+  - copier.py
+
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: copier.py
+        entry: |
+          import os, subprocess, sys
+          msin = sys.argv[1]
+          root = os.path.basename(msin) + '.sector'
+          for i in range(2):
+            msout = f"{root}_{i}"
+            print(f"Copying: {msin} -> {msout}")
+            subprocess.check_call(['cp', '-r', '-L', '--no-preserve=mode', msin, msout])
+
+inputs:
+  - id: msin
+    type: Directory
+    inputBinding:
+      position: 0
+
+outputs:
+  - id: msout
+    type: Directory[]
+    outputBinding:
+      glob: ['$(inputs.msin.basename).sector_*']