ci: raptor build: extract the CWL description and run it

seqan · Apr 28, 2023 · f464e0f · f464e0f
1 parent dbec1e3
commit f464e0f
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Showing 3 changed files with 36 additions and 1 deletion.
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -120,3 +120,16 @@ jobs:
           cd build
           ctest . -j2 --output-on-failure
 
+      - name: Install pipx & cwltool
+        run: |
+          sudo apt-get install --yes pipx
+          pipx install cwltool
+
+      - name: extract CWL descriptions
+        run: |
+          build/bin/raptor build --export-help cwl > raptor/raptor.cwl
+          cd raptor
+          export PATH=$PATH:$PWD/../build/bin
+          cwltool --validate raptor.cwl
+          cwltool raptor.cwl workflow/cwl/tests/raptor-build-0_bins_window_19.yml | tee | grep 2880b1ab21aa50f45ed896cfd470559717094f15
+          cwltool raptor.cwl workflow/cwl/tests/raptor-build-16_bins_window_19.yml | tee | grep 3b802449bf5c611c2f68a8ed86ee3d62e4638af9
diff --git a/src/argument_parsing/build_parsing.cpp b/src/argument_parsing/build_parsing.cpp
@@ -248,13 +248,34 @@ void init_build_parser(sharg::parser & parser, build_arguments & arguments)
                                                          return bins;
                                                       }
                                             )-");
+        auto inputs = node["inputs"];
+        for (std::size_t i = 0; i < inputs.size(); i++)
+        {
+            if (inputs[i]["id"].as<std::string>() == "input")
+            {
+                inputs.remove(i);
+            }
+            if (inputs[i]["id"].as<std::string>() == "output")
+            {
+                inputs[i]["id"] = "output_name";
+            }
+        }
+        node["inputs"].push_back(YAML::Load(R"-(
+                                                id: sequences
+                                                type:
+                                                  type: array
+                                                  items:
+                                                    type: array
+                                                    items: File
+                                               )-"));
         node["outputs"] = YAML::Load(R"-(
                                          index:
                                            type: File
                                            outputBinding:
-                                             glob: $(inputs.output)
+                                             glob: $(inputs.output_name)
                                        )-");
         node["arguments"] = YAML::Load(R"-(
+                                            - --input
                                             - input_bins_filepaths.txt
                                           )-");
     };

diff --git a/workflow/cwl/raptor-build.cwl b/workflow/cwl/raptor-build.cwl
@@ -80,6 +80,7 @@ requirements:
 arguments:
   - prefix: --threads
     valueFrom: $(runtime.cores)
+  - --input
   - input_bins_filepaths.txt
 
 outputs: