Allow creating empty files in initwd (#1118)

* Allow creating empty files in initwd

* Add test for empty file in initwdr.

Author: bogdang989

cwltool/command_line_tool.py

@@ -440,7 +440,7 @@ def rm_pending_output_callback(output_callbacks, jobcachepending,
                             else:
                                 et["entryname"] = None
                             et["writable"] = t.get("writable", False)
-                            if et[u"entry"]:
+                            if et[u"entry"] is not None:
                                 ls.append(et)
                     else:
                         initwd_item = builder.do_eval(t)

tests/test_iwdr.py

@@ -3,7 +3,7 @@
 from cwltool.main import main
 from cwltool import load_tool
 from .util import (get_data, get_windows_safe_factory, windows_needs_docker,
-                   needs_docker, temp_dir, needs_singularity)
+                   needs_docker, temp_dir, needs_singularity, get_main_output)
 
 @windows_needs_docker
 def test_newline_in_entry():
@@ -14,6 +14,16 @@ def test_newline_in_entry():
     echo = factory.make(get_data("tests/wf/iwdr-entry.cwl"))
     assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"}
 
+
+@needs_docker
+def test_empty_file_creation():
+    """
+    test that empty file can be created in InitialWorkingDirectory
+    """
+    err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")])
+    assert err_code == 0
+
+
 @needs_docker
 def test_iwdr_permutations():
     saved_tempdir = tempfile.tempdir

tests/wf/iwdr-empty.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: ["cat", "empty_file"]
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: empty_file
+        entry: ""
+
+inputs: []
+outputs: []