Fix bugs and incorperate version 4.0.0.0

README.md

@@ -109,4 +109,4 @@ You can also run the tests in parallel with `-n` to improve performance
 
 ## Creating a new version
 
-To create a `gatk_cmdline_tools.zip` zip file containing all the generated cwl files for gatk versions 3.5, 3.6, 3.7, 3.8 and 4.beta.6, run `bash build.sh`. This file is uploaded as a release on GitHub for every new release of this package.
+To create a `gatk_cmdline_tools.zip` zip file containing all the generated cwl files for gatk versions 3.5, 3.6, 3.7, 3.8 and 4.0.0.0, run `bash build.sh`. This file is uploaded as a release on GitHub for every new release of this package.

build.sh

@@ -5,7 +5,7 @@ set -euf -o pipefail
 generator_version=$(git describe --tags --always)
 echo "GATK CWL generator: gatk-cwl-generator-${generator_version}"
 
-VERSIONS=( 3.5-0 3.6-0 3.7-0 3.8-0 4.beta.6 )
+VERSIONS=( 3.5-0 3.6-0 3.7-0 3.8-0 4.0.0.0 )
 
 tarbase="gatk-cwl-generator-${generator_version}-gatk_cmdline_tools"
 

gatkcwlgenerator/gen_cwl_arg.py

@@ -170,7 +170,7 @@ def handle_required(typ):
 
     if has_file_type:
         base_cwl_arg["inputBinding"] = {
-            "valueFrom": "$(applyTagsToArgument(\"--{0}\", inputs.{0}_tags))".format(arg_id)
+            "valueFrom": "$(applyTagsToArgument(\"--{0}\", inputs['{0}_tags']))".format(arg_id)
         }
     elif has_array_type:
         base_cwl_arg["inputBinding"] = {

gatkcwlgenerator/tests/test_module.py

@@ -131,23 +131,15 @@ def run_tool(toolname, tool_location, extra_info="", interval=1, filetext=None,
 
 # Unit tests
 
-supported_versions = ["3.5-0", "3.6-0", "3.7-0", "3.8-0", "4.beta.6"]
+supported_versions = ["3.5-0", "3.6-0", "3.7-0", "3.8-0", "4.0.0.0"]
 
 @pytest.mark.skip(reason="""
-The API for gatk is probably going to remain the same for specific versions,
-as this takes a lot of time, it should be disabled generally and used
-for testing added supporting versions for the first time
+The API for gatk is probably going to remain the same for specific versions.
+As this takes a lot of time, it should be disabled generally and used
+for testing added supporting versions for the first time.
 """)
 @pytest.mark.parametrize("version", supported_versions)
 class TestGenerateCWL:
-    def test_get_json_links(self, version):
-        json_links = cwl_gen.get_json_links(version)
-        for link_type, links in json_links.__dict__.items():
-            assert links, "There are no links of type '{}' in gatk version {}".format(
-                    link_type,
-                    version
-                )
-
     def test_no_arguments_in_annotator(self, version):
         # If arguments are in annotator modules, we probably need to add them to the CWL file
         for url in cwl_gen.get_json_links(version).annotator_urls:
@@ -284,7 +276,7 @@ def test_are_cwl_files_valid(cwl_files):
 def test_haplotype_caller(request, HaplotypeCaller_runner):
     HaplotypeCaller_runner()
 
-@pytest.mark.skip("This takes a long time for the gain, so skip it")
+@pytest.mark.skip("This takes too long, so skip it")
 class TestGATKTypes:
     # Test if the haplotype caller accepts all the correct types
     def test_boolean_type(self, HaplotypeCaller_runner):