Merge pull request #29 from NickEngland/nengland/singularity-fix

Fix Crash when using --singularity with Apptainer
hubmapconsortium · Apr 16, 2024 · bc8b747 · bc8b747
2 parents 4277d62 + 60ed964
commit bc8b747
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/cwltool/singularity.py b/cwltool/singularity.py
@@ -58,6 +58,11 @@ def get_version() -> str:
         )
         if _SINGULARITY_VERSION.startswith("singularity version "):
             _SINGULARITY_VERSION = _SINGULARITY_VERSION[20:]
+        if _SINGULARITY_VERSION.startswith("singularity-ce version "):
+            _SINGULARITY_VERSION = _SINGULARITY_VERSION[23:]
+        if _SINGULARITY_VERSION.startswith("apptainer version "):
+            _SINGULARITY_VERSION = _SINGULARITY_VERSION[18:]
+        _logger.debug(f"Singularity version: {_SINGULARITY_VERSION}.")
     return _SINGULARITY_VERSION